Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
On Sat, Dec 21, 2013 at 1:18 AM, epi wrote: > Sorry for the delay in answering, i was out of town. > > i tried gdal directly on the grass dataset, but this custom built gdal > doesn’t have grass-plugin enabled. > > tring to build the grass-pluginn with gdal 1.10.1 and grass7 : > > cd gdal/frmts/grass > make dist > tar -zxvf gdal-grass-1.10.1.tar.gz > cd tar -zxvf gdal-grass-1.10.1 > ./configure --with-gdal=/home/epi/Envs/env1/bin/gdal-config > --with-grass=/home/epi/Envs/env1/grass-7.0.svn/ > > can’t find the grass libs : > > checking for G_asprintf in -lgrass_gis... no > checking for G_putenv in -lgrass_gis.7.0.svn... no ... I don't think that GDAL is already compliant with GRASS 7: See http://trac.osgeo.org/gdal/ticket/2953 If this doesn't hold true, then the GDAL-GRASS plugin code should be re-extracted as a package. To my knowledge the GDAL plugin is nothing else than the source code extraction from main GDAL into a separate package (to be done by the GDAL maintainers). Markus ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
i tried this way : valgrind --tool=memcheck --leak-check=yes --show-reachable=yes --num-callers=20 --track-fds=yes --track-origins=yes r.stream.extract elevation=elevation50m@PERMANENT accumulation=accum threshold=40 stream_rast=stream_network stream_vect=streams —o this the log : https://gist.github.com/27f7666de4eb0cf058b2 On Dec 8, 2013, at 10:46 AM, Maris Nartiss wrote: > As Glynn is pointing to a possible memory problem, I would suggest to > try to run module under valgrind to see any bad fiddling with memory. > > > No help form me, > Maris. > > > 2013/12/8 epi : >> I tried to build gdal from source , without-pt support and rebuild grass >> (without-pg) and pointing it to the newly built gdal. >> >> i had the same problem, same log :( >> >> >> should i try to rebuild libcripto ? >> >> any help in how to debug this problem is greatly appreciated. >> >> Also if you think that other modules (not just r.stream.extract) are >> potentially subject of segfault, let me know and ill try to run them on the >> NC tests dataset. >> >> Thanks, >> >> Massimo. >> >> >> On Dec 7, 2013, at 1:15 PM, epi wrote: >> >>> Hi Glynn, >>> >>> thanks for the detailed explanation! >>> >>> is there something i can try ? >>> >>> perhaps, build gdal from src and disabling postgresql support ? >>> >>> Thanks a lot! >>> >>> Massimo. >>> >>> >>> >>> this a copy of the gdb-backtrace : >>> >>> (gdb) exec-file r.stream.extract elevation=elevation50m@PERMANENT >>> accumulation=accum threshold=40 stream_rast=stream_network >>> stream_vect=streams --o >>> (gdb) r >>> Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract >>> [Thread debugging using libthread_db enabled] >>> Using host libthread_db library >>> "/lib/arm-linux-gnueabihf/libthread_db.so.1". >>> >>> Program received signal SIGILL, Illegal instruction. >>> 0x2c99fe68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 >>> (gdb) bt >>> #0 0x2c99fe68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 >>> Cannot access memory at address 0x0 >>> #1 0x2c99db2c in OPENSSL_cpuid_setup () >>> from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 >>> #2 0x2aab60d6 in call_init (env=0x7efff35c, argv=0x7efff354, argc=1, >>> l=) at dl-init.c:84 >>> #3 call_init (l=, argc=1, argv=0x7efff354, env=0x7efff35c) >>> at dl-init.c:34 >>> #4 0x2aab6158 in _dl_init (main_map=0x2aaca958, argc=1, argv=0x7efff354, >>> env=0x7efff35c) at dl-init.c:133 >>> #5 0x2aaabc62 in _dl_start_user () from /lib/ld-linux-armhf.so.3 >>> #6 0x2aaabc62 in _dl_start_user () from /lib/ld-linux-armhf.so.3 >>> Backtrace stopped: previous frame identical to this frame (corrupt stack?) >>> (gdb) >>> >>> >>> >>> On Dec 6, 2013, at 7:24 PM, Glynn Clements wrote: >>> epi wrote: > googling � > > is it possible that in : > > http://svn.osgeo.org/grass/grass/trunk/raster/r.stream.extract/ > > there may be some assembly code that gets executed which won't work under > armhf ? GRASS doesn't use assembly. And the SIGILL is reported as occurring in libcrypto, not in the GRASS code. The libcrypto dependency typically exists because GDAL links to libpq (PostgreSQL client library) which uses libcrypto for certain authentication methods. libcrypto probably isn't even being used in this situation, so I suspect that a bug is causing either a function pointer or a return address to be corrupted, resulting in a jump to a random memory location which just happens to be inside libcrypto. As r.stream.extract is relatively new, it's possible that it hasn't seen significant testing on platforms other than x86 and x86-64. Apart from anything else, alignment bugs won't show up on those platforms (x86 supports unaligned access, ARM doesn't AFAIK). -- Glynn Clements >>> >> >> ___ >> grass-dev mailing list >> grass-dev@lists.osgeo.org >> http://lists.osgeo.org/mailman/listinfo/grass-dev ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
Sorry for the delay in answering, i was out of town. i tried gdal directly on the grass dataset, but this custom built gdal doesn’t have grass-plugin enabled. tring to build the grass-pluginn with gdal 1.10.1 and grass7 : cd gdal/frmts/grass make dist tar -zxvf gdal-grass-1.10.1.tar.gz cd tar -zxvf gdal-grass-1.10.1 ./configure --with-gdal=/home/epi/Envs/env1/bin/gdal-config --with-grass=/home/epi/Envs/env1/grass-7.0.svn/ can’t find the grass libs : checking for G_asprintf in -lgrass_gis... no checking for G_putenv in -lgrass_gis.7.0.svn... no configure: error: --with-grass=/home/epi/Envs/env1/grass-7.0.svn/ requested, but libraries not found! Perhaps you need to set LD_LIBRARY_PATH to include /home/epi/Envs/env1/grass-7.0.svn//lib? i also tried : export LD_LIBRARY_PATH=/home/epi/Envs/env1/grass-7.0.svn/lib:$LD_LIBRARY_PATH or adding : /home/epi/Envs/env1/grass-7.0.svn/lib in /etc/ld.so.conf.d/grass.conf but i got the same log, i think to remember tahat gdal-grass is not compatible with grass70. in any case I just tried gdalinfo on a standard geotiff (i used the the GTiff from the grass dataset) and it works fine : epi@udoo:~$ which gdalinfo /home/epi/Envs/env1/bin/gdalinfo epi@udoo:~$ cd epi@udoo:~$ gdalinfo basin_50K.tif Driver: GTiff/GeoTIFF Files: basin_50K.tif Size is 1500, 1350 Coordinate System is: PROJCS["Lambert Conformal Conic", GEOGCS["NAD83", DATUM["North_American_Datum_1983", SPHEROID["GRS 1980",6378137,298.2572221010002, AUTHORITY["EPSG","7019"]], AUTHORITY["EPSG","6269"]], PRIMEM["Greenwich",0], UNIT["degree",0.0174532925199433], AUTHORITY["EPSG","4269"]], PROJECTION["Lambert_Conformal_Conic_2SP"], PARAMETER["standard_parallel_1",36.16], PARAMETER["standard_parallel_2",34.34], PARAMETER["latitude_of_origin",33.75], PARAMETER["central_meridian",-79], PARAMETER["false_easting",609601.22], PARAMETER["false_northing",0], UNIT["metre",1, AUTHORITY["EPSG","9001"]]] Origin = (63.000,228500.000) Pixel Size = (10.000,-10.000) Metadata: AREA_OR_POINT=Area Image Structure Metadata: INTERLEAVE=BAND Corner Coordinates: Upper Left ( 63.000, 228500.000) ( 78d46'27.41"W, 35d48'34.59"N) Lower Left ( 63.000, 215000.000) ( 78d46'28.63"W, 35d41'16.54"N) Upper Right ( 645000.000, 228500.000) ( 78d36'29.89"W, 35d48'33.08"N) Lower Right ( 645000.000, 215000.000) ( 78d36'32.01"W, 35d41'15.03"N) Center ( 637500.000, 221750.000) ( 78d41'29.49"W, 35d44'54.91"N) Band 1 Block=1500x1 Type=Int32, ColorInterp=Gray NoData Value=- epi@udoo:~$ On Dec 10, 2013, at 11:22 AM, Glynn Clements wrote: > > epi wrote: > >> thanks for the detailed explanation! >> >> is there something i can try ? > > Does GDAL itself work? Try running one of its utilities, e.g. > gdalinfo. > > -- > Glynn Clements ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
epi wrote: > thanks for the detailed explanation! > > is there something i can try ? Does GDAL itself work? Try running one of its utilities, e.g. gdalinfo. -- Glynn Clements ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
As Glynn is pointing to a possible memory problem, I would suggest to try to run module under valgrind to see any bad fiddling with memory. No help form me, Maris. 2013/12/8 epi : > I tried to build gdal from source , without-pt support and rebuild grass > (without-pg) and pointing it to the newly built gdal. > > i had the same problem, same log :( > > > should i try to rebuild libcripto ? > > any help in how to debug this problem is greatly appreciated. > > Also if you think that other modules (not just r.stream.extract) are > potentially subject of segfault, let me know and ill try to run them on the > NC tests dataset. > > Thanks, > > Massimo. > > > On Dec 7, 2013, at 1:15 PM, epi wrote: > >> Hi Glynn, >> >> thanks for the detailed explanation! >> >> is there something i can try ? >> >> perhaps, build gdal from src and disabling postgresql support ? >> >> Thanks a lot! >> >> Massimo. >> >> >> >> this a copy of the gdb-backtrace : >> >> (gdb) exec-file r.stream.extract elevation=elevation50m@PERMANENT >> accumulation=accum threshold=40 stream_rast=stream_network >> stream_vect=streams --o >> (gdb) r >> Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract >> [Thread debugging using libthread_db enabled] >> Using host libthread_db library "/lib/arm-linux-gnueabihf/libthread_db.so.1". >> >> Program received signal SIGILL, Illegal instruction. >> 0x2c99fe68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 >> (gdb) bt >> #0 0x2c99fe68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 >> Cannot access memory at address 0x0 >> #1 0x2c99db2c in OPENSSL_cpuid_setup () >> from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 >> #2 0x2aab60d6 in call_init (env=0x7efff35c, argv=0x7efff354, argc=1, >>l=) at dl-init.c:84 >> #3 call_init (l=, argc=1, argv=0x7efff354, env=0x7efff35c) >>at dl-init.c:34 >> #4 0x2aab6158 in _dl_init (main_map=0x2aaca958, argc=1, argv=0x7efff354, >>env=0x7efff35c) at dl-init.c:133 >> #5 0x2aaabc62 in _dl_start_user () from /lib/ld-linux-armhf.so.3 >> #6 0x2aaabc62 in _dl_start_user () from /lib/ld-linux-armhf.so.3 >> Backtrace stopped: previous frame identical to this frame (corrupt stack?) >> (gdb) >> >> >> >> On Dec 6, 2013, at 7:24 PM, Glynn Clements wrote: >> >>> >>> epi wrote: >>> googling � is it possible that in : http://svn.osgeo.org/grass/grass/trunk/raster/r.stream.extract/ there may be some assembly code that gets executed which won't work under armhf ? >>> >>> GRASS doesn't use assembly. And the SIGILL is reported as occurring in >>> libcrypto, not in the GRASS code. >>> >>> The libcrypto dependency typically exists because GDAL links to libpq >>> (PostgreSQL client library) which uses libcrypto for certain >>> authentication methods. >>> >>> libcrypto probably isn't even being used in this situation, so I >>> suspect that a bug is causing either a function pointer or a return >>> address to be corrupted, resulting in a jump to a random memory >>> location which just happens to be inside libcrypto. >>> >>> As r.stream.extract is relatively new, it's possible that it hasn't >>> seen significant testing on platforms other than x86 and x86-64. Apart >>> from anything else, alignment bugs won't show up on those platforms >>> (x86 supports unaligned access, ARM doesn't AFAIK). >>> >>> -- >>> Glynn Clements >> > > ___ > grass-dev mailing list > grass-dev@lists.osgeo.org > http://lists.osgeo.org/mailman/listinfo/grass-dev ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
I tried to build gdal from source , without-pt support and rebuild grass (without-pg) and pointing it to the newly built gdal. i had the same problem, same log :( should i try to rebuild libcripto ? any help in how to debug this problem is greatly appreciated. Also if you think that other modules (not just r.stream.extract) are potentially subject of segfault, let me know and ill try to run them on the NC tests dataset. Thanks, Massimo. On Dec 7, 2013, at 1:15 PM, epi wrote: > Hi Glynn, > > thanks for the detailed explanation! > > is there something i can try ? > > perhaps, build gdal from src and disabling postgresql support ? > > Thanks a lot! > > Massimo. > > > > this a copy of the gdb-backtrace : > > (gdb) exec-file r.stream.extract elevation=elevation50m@PERMANENT > accumulation=accum threshold=40 stream_rast=stream_network > stream_vect=streams --o > (gdb) r > Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract > [Thread debugging using libthread_db enabled] > Using host libthread_db library "/lib/arm-linux-gnueabihf/libthread_db.so.1". > > Program received signal SIGILL, Illegal instruction. > 0x2c99fe68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 > (gdb) bt > #0 0x2c99fe68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 > Cannot access memory at address 0x0 > #1 0x2c99db2c in OPENSSL_cpuid_setup () > from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 > #2 0x2aab60d6 in call_init (env=0x7efff35c, argv=0x7efff354, argc=1, >l=) at dl-init.c:84 > #3 call_init (l=, argc=1, argv=0x7efff354, env=0x7efff35c) >at dl-init.c:34 > #4 0x2aab6158 in _dl_init (main_map=0x2aaca958, argc=1, argv=0x7efff354, >env=0x7efff35c) at dl-init.c:133 > #5 0x2aaabc62 in _dl_start_user () from /lib/ld-linux-armhf.so.3 > #6 0x2aaabc62 in _dl_start_user () from /lib/ld-linux-armhf.so.3 > Backtrace stopped: previous frame identical to this frame (corrupt stack?) > (gdb) > > > > On Dec 6, 2013, at 7:24 PM, Glynn Clements wrote: > >> >> epi wrote: >> >>> googling � >>> >>> is it possible that in : >>> >>> http://svn.osgeo.org/grass/grass/trunk/raster/r.stream.extract/ >>> >>> there may be some assembly code that gets executed which won't work under >>> armhf ? >> >> GRASS doesn't use assembly. And the SIGILL is reported as occurring in >> libcrypto, not in the GRASS code. >> >> The libcrypto dependency typically exists because GDAL links to libpq >> (PostgreSQL client library) which uses libcrypto for certain >> authentication methods. >> >> libcrypto probably isn't even being used in this situation, so I >> suspect that a bug is causing either a function pointer or a return >> address to be corrupted, resulting in a jump to a random memory >> location which just happens to be inside libcrypto. >> >> As r.stream.extract is relatively new, it's possible that it hasn't >> seen significant testing on platforms other than x86 and x86-64. Apart >> from anything else, alignment bugs won't show up on those platforms >> (x86 supports unaligned access, ARM doesn't AFAIK). >> >> -- >> Glynn Clements > ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
Hi Glynn, thanks for the detailed explanation! is there something i can try ? perhaps, build gdal from src and disabling postgresql support ? Thanks a lot! Massimo. this a copy of the gdb-backtrace : (gdb) exec-file r.stream.extract elevation=elevation50m@PERMANENT accumulation=accum threshold=40 stream_rast=stream_network stream_vect=streams --o (gdb) r Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/arm-linux-gnueabihf/libthread_db.so.1". Program received signal SIGILL, Illegal instruction. 0x2c99fe68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 (gdb) bt #0 0x2c99fe68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 Cannot access memory at address 0x0 #1 0x2c99db2c in OPENSSL_cpuid_setup () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 #2 0x2aab60d6 in call_init (env=0x7efff35c, argv=0x7efff354, argc=1, l=) at dl-init.c:84 #3 call_init (l=, argc=1, argv=0x7efff354, env=0x7efff35c) at dl-init.c:34 #4 0x2aab6158 in _dl_init (main_map=0x2aaca958, argc=1, argv=0x7efff354, env=0x7efff35c) at dl-init.c:133 #5 0x2aaabc62 in _dl_start_user () from /lib/ld-linux-armhf.so.3 #6 0x2aaabc62 in _dl_start_user () from /lib/ld-linux-armhf.so.3 Backtrace stopped: previous frame identical to this frame (corrupt stack?) (gdb) On Dec 6, 2013, at 7:24 PM, Glynn Clements wrote: > > epi wrote: > >> googling � >> >> is it possible that in : >> >> http://svn.osgeo.org/grass/grass/trunk/raster/r.stream.extract/ >> >> there may be some assembly code that gets executed which won't work under >> armhf ? > > GRASS doesn't use assembly. And the SIGILL is reported as occurring in > libcrypto, not in the GRASS code. > > The libcrypto dependency typically exists because GDAL links to libpq > (PostgreSQL client library) which uses libcrypto for certain > authentication methods. > > libcrypto probably isn't even being used in this situation, so I > suspect that a bug is causing either a function pointer or a return > address to be corrupted, resulting in a jump to a random memory > location which just happens to be inside libcrypto. > > As r.stream.extract is relatively new, it's possible that it hasn't > seen significant testing on platforms other than x86 and x86-64. Apart > from anything else, alignment bugs won't show up on those platforms > (x86 supports unaligned access, ARM doesn't AFAIK). > > -- > Glynn Clements ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
Hi Maris, this is the bt : (gdb) exec-file r.stream.extract elevation=elevation50m@PERMANENT accumulation=accum threshold=40 stream_rast=stream_network stream_vect=streams --o (gdb) r Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/arm-linux-gnueabihf/libthread_db.so.1". Program received signal SIGILL, Illegal instruction. 0x2c99fe68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 (gdb) bt #0 0x2c99fe68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 Cannot access memory at address 0x0 #1 0x2c99db2c in OPENSSL_cpuid_setup () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 #2 0x2aab60d6 in call_init (env=0x7efff35c, argv=0x7efff354, argc=1, l=) at dl-init.c:84 #3 call_init (l=, argc=1, argv=0x7efff354, env=0x7efff35c) at dl-init.c:34 #4 0x2aab6158 in _dl_init (main_map=0x2aaca958, argc=1, argv=0x7efff354, env=0x7efff35c) at dl-init.c:133 #5 0x2aaabc62 in _dl_start_user () from /lib/ld-linux-armhf.so.3 #6 0x2aaabc62 in _dl_start_user () from /lib/ld-linux-armhf.so.3 Backtrace stopped: previous frame identical to this frame (corrupt stack?) (gdb) rebuilding with : gcc -g -Wall -O0 gave me no worning in r.stream.extract On Dec 6, 2013, at 6:36 PM, Maris Nartiss wrote: > Any warnings during compilation? > Try to compile with -g and -O0 to get slow but debugging-friendly version. > > When program gets stopped by SIGILL in gdb, issue "bt" command to get > backtrace. > > No help form me, but more info never hurts ;) > > Maris. > > > 2013/12/6 epi : >> Hi ! >> >> this the output of gdb : >> >> Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract >> .stream.extract elevation=elevation50m@PERMANENT accumulation=accum >> threshold=40 stream_rast=stream_network stream_vect=streams --o >> [Thread debugging using libthread_db enabled] >> Using host libthread_db library >> "/lib/arm-linux-gnueabihf/libthread_db.so.1". >> >> Program received signal SIGILL, Illegal instruction. >> 0x2c966e68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 >> (gdb) >> >> >> Thanks for your help! >> >> >> Massimo. >> >> >> On Dec 6, 2013, at 4:16 PM, Rashad M wrote: >> >> Hello Massimo, >> >> A gdb output could be more helpful for a segfault >> >> >> On Fri, Dec 6, 2013 at 7:06 PM, epi wrote: >>> >>> Hi, >>> >>> i’m trying to run “r.stream.extract” on a little linux machine, i got got >>> grass up and running on a small quad-core Arm 1gb ram >>> OS : Debian SID ArmHF. >>> >>> the command i’m using is : >>> >>> r.stream.extract elevation=elevation@PERMANENT accumulation=accum >>> threshold=40 stream_rast=stream_network stream_vect=streams --o --q >>> >>> location : nc_spm_08_grass7/PERMANENT/ >>> >>> >>> i set the debug level to 5, this the segfault log : >>> >>> https://gist.github.com/epifanio/7829206 >>> >>> if helpful, this is the log of make clean and make : >>> >>> https://gist.github.com/epifanio/7829256 >>> >>> On other platform (same grass and r.stream.extract version it wks just >>> fine) >>> Have you any idea on what’s wrong ? >>> >>> Thanks, >>> >>> Massimo. >>> >>> ___ >>> grass-dev mailing list >>> grass-dev@lists.osgeo.org >>> http://lists.osgeo.org/mailman/listinfo/grass-dev >> >> >> >> >> -- >> Regards, >> Rashad >> >> >> >> ___ >> grass-dev mailing list >> grass-dev@lists.osgeo.org >> http://lists.osgeo.org/mailman/listinfo/grass-dev ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
epi wrote: > googling � > > is it possible that in : > > http://svn.osgeo.org/grass/grass/trunk/raster/r.stream.extract/ > > there may be some assembly code that gets executed which won't work under > armhf ? GRASS doesn't use assembly. And the SIGILL is reported as occurring in libcrypto, not in the GRASS code. The libcrypto dependency typically exists because GDAL links to libpq (PostgreSQL client library) which uses libcrypto for certain authentication methods. libcrypto probably isn't even being used in this situation, so I suspect that a bug is causing either a function pointer or a return address to be corrupted, resulting in a jump to a random memory location which just happens to be inside libcrypto. As r.stream.extract is relatively new, it's possible that it hasn't seen significant testing on platforms other than x86 and x86-64. Apart from anything else, alignment bugs won't show up on those platforms (x86 supports unaligned access, ARM doesn't AFAIK). -- Glynn Clements ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
Any warnings during compilation? Try to compile with -g and -O0 to get slow but debugging-friendly version. When program gets stopped by SIGILL in gdb, issue "bt" command to get backtrace. No help form me, but more info never hurts ;) Maris. 2013/12/6 epi : > Hi ! > > this the output of gdb : > > Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract > .stream.extract elevation=elevation50m@PERMANENT accumulation=accum > threshold=40 stream_rast=stream_network stream_vect=streams --o > [Thread debugging using libthread_db enabled] > Using host libthread_db library > "/lib/arm-linux-gnueabihf/libthread_db.so.1". > > Program received signal SIGILL, Illegal instruction. > 0x2c966e68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 > (gdb) > > > Thanks for your help! > > > Massimo. > > > On Dec 6, 2013, at 4:16 PM, Rashad M wrote: > > Hello Massimo, > > A gdb output could be more helpful for a segfault > > > On Fri, Dec 6, 2013 at 7:06 PM, epi wrote: >> >> Hi, >> >> i’m trying to run “r.stream.extract” on a little linux machine, i got got >> grass up and running on a small quad-core Arm 1gb ram >> OS : Debian SID ArmHF. >> >> the command i’m using is : >> >> r.stream.extract elevation=elevation@PERMANENT accumulation=accum >> threshold=40 stream_rast=stream_network stream_vect=streams --o --q >> >> location : nc_spm_08_grass7/PERMANENT/ >> >> >> i set the debug level to 5, this the segfault log : >> >> https://gist.github.com/epifanio/7829206 >> >> if helpful, this is the log of make clean and make : >> >> https://gist.github.com/epifanio/7829256 >> >> On other platform (same grass and r.stream.extract version it wks just >> fine) >> Have you any idea on what’s wrong ? >> >> Thanks, >> >> Massimo. >> >> ___ >> grass-dev mailing list >> grass-dev@lists.osgeo.org >> http://lists.osgeo.org/mailman/listinfo/grass-dev > > > > > -- > Regards, >Rashad > > > > ___ > grass-dev mailing list > grass-dev@lists.osgeo.org > http://lists.osgeo.org/mailman/listinfo/grass-dev ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
i tried to rebuild grass with CFLAGS='-g -Wal’ CXXFLAGS='-g -Wal’ this the full log : https://gist.github.com/epifanio/7833957 On Dec 6, 2013, at 5:18 PM, epi wrote: > googling … > > is it possible that in : > > http://svn.osgeo.org/grass/grass/trunk/raster/r.stream.extract/ > > there may be some assembly code that gets executed which won't work under > armhf ? > > Massimo. > > > > On Dec 6, 2013, at 4:37 PM, epi wrote: > >> i tried to add : >> handle SIGILL nostop >> to have more debug .. >> >> i can’t understand the log :/ >> >> >> (gdb) handle SIGILL nostop >> SignalStop Print Pass to program Description >> SIGILLNo Yes Yes Illegal instruction >> (gdb) >> >> >> >> >> (gdb) exec-file r.stream.extract elevation=elevation@PERMANENT >> accumulation=accum threshold=20 stream_rast=stream_network >> stream_vect=streams --o >> (gdb) r >> Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract >> .stream.extract elevation=elevation50m@PERMANENT accumulation=accum >> threshold=40 stream_rast=stream_network stream_vect=streams --o >> [Thread debugging using libthread_db enabled] >> Using host libthread_db library "/lib/arm-linux-gnueabihf/libthread_db.so.1". >> >> Program received signal SIGILL, Illegal instruction. >> D2/5: G_file_name(): path = >> /home/epi/Envs/grass7data/nc_spm_08_grass7/PERMANENT >> >> Description: >> Performs stream network extraction. >> >> Keywords: >> raster, hydrology, stream network >> >> Usage: >> r.stream.extract elevation=name [accumulation=name] [depression=name] >>threshold=value [d8cut=value] [mexp=value] [stream_length=value] >>[memory=value] [stream_rast=name] [stream_vect=name] [direction=name] >>[--overwrite] [--verbose] [--quiet] >> >> Flags: >> --o Allow output files to overwrite existing files >> --v Verbose module output >> --q Quiet module output >> >> Parameters: >> elevation Name of input elevation raster map >>accumulation Name of input accumulation raster map >>Stream extraction will use provided accumulation instead >> of calculating it a new >> depression Name of raster map with real depressions >>Streams will not be routed out of real depressions >> threshold Minimum flow accumulation for streams >>Must be > 0 >> d8cut Use SFD above this threshold >>If accumulation is larger than d8cut, SFD is used instead >> of MFD. Applies only if no accumulation map is given. >> default: infinity >>mexp Montgomery exponent for slope, disabled with 0 >>Montgomery: accumulation is multiplied with >> pow(slope,mexp) and then compared with threshold. >> default: 0 >> stream_length Delete stream segments shorter than stream_length cells. >>Applies only to first-order stream segments >> (springs/stream heads). >> default: 0 >> memory Maximum memory to be used in MB >> default: 300 >> stream_rast Name for output raster map with unique stream ids >> stream_vect Name for output vector map with unique stream ids >> direction Name for output raster map with flow direction >> >> ERROR: Option does not accept multiple answers >> [Inferior 1 (process 7565) exited with code 01] >> (gdb) >> >> >> >> On Dec 6, 2013, at 4:32 PM, epi wrote: >> >>> Hi ! >>> >>> this the output of gdb : >>> >>> Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract >>> .stream.extract elevation=elevation50m@PERMANENT accumulation=accum >>> threshold=40 stream_rast=stream_network stream_vect=streams --o >>> [Thread debugging using libthread_db enabled] >>> Using host libthread_db library >>> "/lib/arm-linux-gnueabihf/libthread_db.so.1". >>> >>> Program received signal SIGILL, Illegal instruction. >>> 0x2c966e68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 >>> (gdb) >>> >>> >>> Thanks for your help! >>> >>> >>> Massimo. >>> >>> >>> On Dec 6, 2013, at 4:16 PM, Rashad M wrote: >>> Hello Massimo, A gdb output could be more helpful for a segfault On Fri, Dec 6, 2013 at 7:06 PM, epi wrote: Hi, i’m trying to run “r.stream.extract” on a little linux machine, i got got grass up and running on a small quad-core Arm 1gb ram OS : Debian SID ArmHF. the command i’m using is : r.stream.extract elevation=elevation@PERMANENT accumulation=accum threshold=40 stream_rast=stream_network stream_vect=streams --o --q location : nc_spm_08_grass7/PERMANENT/ i set the debug level to 5, this the segfault log : https://gist.github.com/epifanio/7829206 if helpful, this is the log of make clean and make : https://gist.github.com/epifanio/7829
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
googling … is it possible that in : http://svn.osgeo.org/grass/grass/trunk/raster/r.stream.extract/ there may be some assembly code that gets executed which won't work under armhf ? Massimo. On Dec 6, 2013, at 4:37 PM, epi wrote: > i tried to add : > handle SIGILL nostop > to have more debug .. > > i can’t understand the log :/ > > > (gdb) handle SIGILL nostop > SignalStopPrint Pass to program Description > SIGILLNo Yes Yes Illegal instruction > (gdb) > > > > > (gdb) exec-file r.stream.extract elevation=elevation@PERMANENT > accumulation=accum threshold=20 stream_rast=stream_network > stream_vect=streams --o > (gdb) r > Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract > .stream.extract elevation=elevation50m@PERMANENT accumulation=accum > threshold=40 stream_rast=stream_network stream_vect=streams --o > [Thread debugging using libthread_db enabled] > Using host libthread_db library "/lib/arm-linux-gnueabihf/libthread_db.so.1". > > Program received signal SIGILL, Illegal instruction. > D2/5: G_file_name(): path = > /home/epi/Envs/grass7data/nc_spm_08_grass7/PERMANENT > > Description: > Performs stream network extraction. > > Keywords: > raster, hydrology, stream network > > Usage: > r.stream.extract elevation=name [accumulation=name] [depression=name] >threshold=value [d8cut=value] [mexp=value] [stream_length=value] >[memory=value] [stream_rast=name] [stream_vect=name] [direction=name] >[--overwrite] [--verbose] [--quiet] > > Flags: > --o Allow output files to overwrite existing files > --v Verbose module output > --q Quiet module output > > Parameters: > elevation Name of input elevation raster map >accumulation Name of input accumulation raster map >Stream extraction will use provided accumulation instead > of calculating it a new > depression Name of raster map with real depressions >Streams will not be routed out of real depressions > threshold Minimum flow accumulation for streams >Must be > 0 > d8cut Use SFD above this threshold >If accumulation is larger than d8cut, SFD is used instead > of MFD. Applies only if no accumulation map is given. > default: infinity >mexp Montgomery exponent for slope, disabled with 0 >Montgomery: accumulation is multiplied with > pow(slope,mexp) and then compared with threshold. > default: 0 > stream_length Delete stream segments shorter than stream_length cells. >Applies only to first-order stream segments > (springs/stream heads). > default: 0 > memory Maximum memory to be used in MB > default: 300 > stream_rast Name for output raster map with unique stream ids > stream_vect Name for output vector map with unique stream ids > direction Name for output raster map with flow direction > > ERROR: Option does not accept multiple answers > [Inferior 1 (process 7565) exited with code 01] > (gdb) > > > > On Dec 6, 2013, at 4:32 PM, epi wrote: > >> Hi ! >> >> this the output of gdb : >> >> Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract >> .stream.extract elevation=elevation50m@PERMANENT accumulation=accum >> threshold=40 stream_rast=stream_network stream_vect=streams --o >> [Thread debugging using libthread_db enabled] >> Using host libthread_db library "/lib/arm-linux-gnueabihf/libthread_db.so.1". >> >> Program received signal SIGILL, Illegal instruction. >> 0x2c966e68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 >> (gdb) >> >> >> Thanks for your help! >> >> >> Massimo. >> >> >> On Dec 6, 2013, at 4:16 PM, Rashad M wrote: >> >>> Hello Massimo, >>> >>> A gdb output could be more helpful for a segfault >>> >>> >>> On Fri, Dec 6, 2013 at 7:06 PM, epi wrote: >>> Hi, >>> >>> i’m trying to run “r.stream.extract” on a little linux machine, i got got >>> grass up and running on a small quad-core Arm 1gb ram >>> OS : Debian SID ArmHF. >>> >>> the command i’m using is : >>> >>> r.stream.extract elevation=elevation@PERMANENT accumulation=accum >>> threshold=40 stream_rast=stream_network stream_vect=streams --o --q >>> >>> location : nc_spm_08_grass7/PERMANENT/ >>> >>> >>> i set the debug level to 5, this the segfault log : >>> >>> https://gist.github.com/epifanio/7829206 >>> >>> if helpful, this is the log of make clean and make : >>> >>> https://gist.github.com/epifanio/7829256 >>> >>> On other platform (same grass and r.stream.extract version it wks just fine) >>> Have you any idea on what’s wrong ? >>> >>> Thanks, >>> >>> Massimo. >>> >>> ___ >>> grass-dev mailing list >>> grass-dev@lists.osgeo.org >>> http://lists.osgeo.org/mailman/listinfo/grass-dev >>> >
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
i tried to add : handle SIGILL nostop to have more debug .. i can’t understand the log :/ (gdb) handle SIGILL nostop SignalStop Print Pass to program Description SIGILLNoYes Yes Illegal instruction (gdb) (gdb) exec-file r.stream.extract elevation=elevation@PERMANENT accumulation=accum threshold=20 stream_rast=stream_network stream_vect=streams --o (gdb) r Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract .stream.extract elevation=elevation50m@PERMANENT accumulation=accum threshold=40 stream_rast=stream_network stream_vect=streams --o [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/arm-linux-gnueabihf/libthread_db.so.1". Program received signal SIGILL, Illegal instruction. D2/5: G_file_name(): path = /home/epi/Envs/grass7data/nc_spm_08_grass7/PERMANENT Description: Performs stream network extraction. Keywords: raster, hydrology, stream network Usage: r.stream.extract elevation=name [accumulation=name] [depression=name] threshold=value [d8cut=value] [mexp=value] [stream_length=value] [memory=value] [stream_rast=name] [stream_vect=name] [direction=name] [--overwrite] [--verbose] [--quiet] Flags: --o Allow output files to overwrite existing files --v Verbose module output --q Quiet module output Parameters: elevation Name of input elevation raster map accumulation Name of input accumulation raster map Stream extraction will use provided accumulation instead of calculating it a new depression Name of raster map with real depressions Streams will not be routed out of real depressions threshold Minimum flow accumulation for streams Must be > 0 d8cut Use SFD above this threshold If accumulation is larger than d8cut, SFD is used instead of MFD. Applies only if no accumulation map is given. default: infinity mexp Montgomery exponent for slope, disabled with 0 Montgomery: accumulation is multiplied with pow(slope,mexp) and then compared with threshold. default: 0 stream_length Delete stream segments shorter than stream_length cells. Applies only to first-order stream segments (springs/stream heads). default: 0 memory Maximum memory to be used in MB default: 300 stream_rast Name for output raster map with unique stream ids stream_vect Name for output vector map with unique stream ids direction Name for output raster map with flow direction ERROR: Option does not accept multiple answers [Inferior 1 (process 7565) exited with code 01] (gdb) On Dec 6, 2013, at 4:32 PM, epi wrote: > Hi ! > > this the output of gdb : > > Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract > .stream.extract elevation=elevation50m@PERMANENT accumulation=accum > threshold=40 stream_rast=stream_network stream_vect=streams --o > [Thread debugging using libthread_db enabled] > Using host libthread_db library "/lib/arm-linux-gnueabihf/libthread_db.so.1". > > Program received signal SIGILL, Illegal instruction. > 0x2c966e68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 > (gdb) > > > Thanks for your help! > > > Massimo. > > > On Dec 6, 2013, at 4:16 PM, Rashad M wrote: > >> Hello Massimo, >> >> A gdb output could be more helpful for a segfault >> >> >> On Fri, Dec 6, 2013 at 7:06 PM, epi wrote: >> Hi, >> >> i’m trying to run “r.stream.extract” on a little linux machine, i got got >> grass up and running on a small quad-core Arm 1gb ram >> OS : Debian SID ArmHF. >> >> the command i’m using is : >> >> r.stream.extract elevation=elevation@PERMANENT accumulation=accum >> threshold=40 stream_rast=stream_network stream_vect=streams --o --q >> >> location : nc_spm_08_grass7/PERMANENT/ >> >> >> i set the debug level to 5, this the segfault log : >> >> https://gist.github.com/epifanio/7829206 >> >> if helpful, this is the log of make clean and make : >> >> https://gist.github.com/epifanio/7829256 >> >> On other platform (same grass and r.stream.extract version it wks just fine) >> Have you any idea on what’s wrong ? >> >> Thanks, >> >> Massimo. >> >> ___ >> grass-dev mailing list >> grass-dev@lists.osgeo.org >> http://lists.osgeo.org/mailman/listinfo/grass-dev >> >> >> >> -- >> Regards, >>Rashad > ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
Hi ! this the output of gdb : Starting program: /home/epi/Envs/env1/grass-7.0.svn/bin/r.stream.extract .stream.extract elevation=elevation50m@PERMANENT accumulation=accum threshold=40 stream_rast=stream_network stream_vect=streams --o [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/arm-linux-gnueabihf/libthread_db.so.1". Program received signal SIGILL, Illegal instruction. 0x2c966e68 in ?? () from /usr/lib/arm-linux-gnueabihf/libcrypto.so.1.0.0 (gdb) Thanks for your help! Massimo. On Dec 6, 2013, at 4:16 PM, Rashad M wrote: > Hello Massimo, > > A gdb output could be more helpful for a segfault > > > On Fri, Dec 6, 2013 at 7:06 PM, epi wrote: > Hi, > > i’m trying to run “r.stream.extract” on a little linux machine, i got got > grass up and running on a small quad-core Arm 1gb ram > OS : Debian SID ArmHF. > > the command i’m using is : > > r.stream.extract elevation=elevation@PERMANENT accumulation=accum > threshold=40 stream_rast=stream_network stream_vect=streams --o --q > > location : nc_spm_08_grass7/PERMANENT/ > > > i set the debug level to 5, this the segfault log : > > https://gist.github.com/epifanio/7829206 > > if helpful, this is the log of make clean and make : > > https://gist.github.com/epifanio/7829256 > > On other platform (same grass and r.stream.extract version it wks just fine) > Have you any idea on what’s wrong ? > > Thanks, > > Massimo. > > ___ > grass-dev mailing list > grass-dev@lists.osgeo.org > http://lists.osgeo.org/mailman/listinfo/grass-dev > > > > -- > Regards, >Rashad ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
Re: [GRASS-dev] segfault on 'r.stream.extract' - debian armh
Hello Massimo, A gdb output could be more helpful for a segfault On Fri, Dec 6, 2013 at 7:06 PM, epi wrote: > Hi, > > i’m trying to run “r.stream.extract” on a little linux machine, i got got > grass up and running on a small quad-core Arm 1gb ram > OS : Debian SID ArmHF. > > the command i’m using is : > > r.stream.extract elevation=elevation@PERMANENT accumulation=accum > threshold=40 stream_rast=stream_network stream_vect=streams --o --q > > location : nc_spm_08_grass7/PERMANENT/ > > > i set the debug level to 5, this the segfault log : > > https://gist.github.com/epifanio/7829206 > > if helpful, this is the log of make clean and make : > > https://gist.github.com/epifanio/7829256 > > On other platform (same grass and r.stream.extract version it wks just > fine) > Have you any idea on what’s wrong ? > > Thanks, > > Massimo. > > ___ > grass-dev mailing list > grass-dev@lists.osgeo.org > http://lists.osgeo.org/mailman/listinfo/grass-dev > -- Regards, Rashad ___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
[GRASS-dev] segfault on 'r.stream.extract' - debian armh
Hi, i’m trying to run “r.stream.extract” on a little linux machine, i got got grass up and running on a small quad-core Arm 1gb ram OS : Debian SID ArmHF. the command i’m using is : r.stream.extract elevation=elevation@PERMANENT accumulation=accum threshold=40 stream_rast=stream_network stream_vect=streams --o --q location : nc_spm_08_grass7/PERMANENT/ i set the debug level to 5, this the segfault log : https://gist.github.com/epifanio/7829206 if helpful, this is the log of make clean and make : https://gist.github.com/epifanio/7829256 On other platform (same grass and r.stream.extract version it wks just fine) Have you any idea on what’s wrong ? Thanks, Massimo.___ grass-dev mailing list grass-dev@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-dev
