Re: [GRASS-user] r.li help
Nathan Lemoine wrote: I've tried running gdb on the r.li.patchnum program, but I have no debugging or programming experience, so I can only report the error messages I've received. running the program normally, without of gdb, gets me the error: Illegal filename. Character not allowed. Illegal filename. Character not allowed. Illegal filename. Character not allowed. WARNING: Unable to open header file for raster map @(null) CHILD[pid = 326]: unable to open mask ... continue without!!! this error message typically just repeats itself. running the program with gdb gets me: Starting program: /Applications/GRASS-6.4.app/Contents/MacOS/bin/r.li.patchnum .li.patchnum map=northrast conf=whole out=test Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_INVALID_ADDRESS at address: 0x0008 0x7fff806b0964 in strcmp () and if I backtrace: (gdb) bt #0 0x7fff806b0964 in strcmp () #1 0x00010005bc63 in parseSetup () #2 0x00010005c899 in calculateIndex () #3 0x000108c8 in start () you've done well with the backtrace Nathan, after so many months we finally know where this bug is. I think Paolo might buy you a beer. (gdb on Linux didn't give me much to go on, only that it finished with error code 1) see https://trac.osgeo.org/grass/ticket/718#comment:16 r.li.daemon is using strtok() in its multi-thread code, but that function is not safe to use with threads and so the jobs collide and the program breaks. Because r.li.daemon always starts 10 jobs, it breaks even if you don't have a multi-processor CPU. The strtok() function uses a static buffer while parsing, so it's not thread safe. It doesn't look like it will be very hard to fix, but it's slightly beyond my talents to do so. Hamish ps- for future reference, if you use bt full in gdb you get the value of all variables, and if you type l you see which line in the source code it got to. http://grass.osgeo.org/wiki/Bugs#Using_GDB ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] r.li help
per Hamish I used some more gdb commands and got some more information: (gdb) r.li.patchnum map=northrast conf=whole output=test Starting program: /Applications/GRASS-6.4.app/Contents/MacOS/bin/ r.li.patchnum .li.patchnum map=northrast conf=whole output=test Reading symbols for shared libraries .++. done Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_INVALID_ADDRESS at address: 0x0008 0x7fff806b0964 in strcmp () (gdb) bt full #0 0x7fff806b0964 in strcmp () No symbol table info available. #1 0x00010005bc63 in parseSetup () No symbol table info available. #2 0x00010005c899 in calculateIndex () No symbol table info available. #3 0x000108c8 in start () No symbol table info available. (gdb) l 1 /var/tmp//cc9BQQ7d.s: No such file or directory. in /var/tmp//cc9BQQ7d.s (gdb) frame 2 #2 0x00010005c899 in calculateIndex () (gdb) l 1 in /var/tmp//cc9BQQ7d.s it looks like this is the file where the information is getting lost. i hope this helps a bit more. On Aug 17, 2009, at 2:35 AM, Hamish wrote: Nathan Lemoine wrote: I've tried running gdb on the r.li.patchnum program, but I have no debugging or programming experience, so I can only report the error messages I've received. running the program normally, without of gdb, gets me the error: Illegal filename. Character not allowed. Illegal filename. Character not allowed. Illegal filename. Character not allowed. WARNING: Unable to open header file for raster map @(null) CHILD[pid = 326]: unable to open mask ... continue without!!! this error message typically just repeats itself. running the program with gdb gets me: Starting program: /Applications/GRASS-6.4.app/Contents/MacOS/bin/ r.li.patchnum .li.patchnum map=northrast conf=whole out=test Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_INVALID_ADDRESS at address: 0x0008 0x7fff806b0964 in strcmp () and if I backtrace: (gdb) bt #0 0x7fff806b0964 in strcmp () #1 0x00010005bc63 in parseSetup () #2 0x00010005c899 in calculateIndex () #3 0x000108c8 in start () you've done well with the backtrace Nathan, after so many months we finally know where this bug is. I think Paolo might buy you a beer. (gdb on Linux didn't give me much to go on, only that it finished with error code 1) see https://trac.osgeo.org/grass/ticket/718#comment:16 r.li.daemon is using strtok() in its multi-thread code, but that function is not safe to use with threads and so the jobs collide and the program breaks. Because r.li.daemon always starts 10 jobs, it breaks even if you don't have a multi-processor CPU. The strtok() function uses a static buffer while parsing, so it's not thread safe. It doesn't look like it will be very hard to fix, but it's slightly beyond my talents to do so. Hamish ps- for future reference, if you use bt full in gdb you get the value of all variables, and if you type l you see which line in the source code it got to. http://grass.osgeo.org/wiki/Bugs#Using_GDB ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] r.li help
I've tried running gdb on the r.li.patchnum program, but I have no debugging or programming experience, so I can only report the error messages I've received. running the program normally, without of gdb, gets me the error: Illegal filename. Character not allowed. Illegal filename. Character not allowed. Illegal filename. Character not allowed. WARNING: Unable to open header file for raster map @(null) CHILD[pid = 326]: unable to open mask ... continue without!!! this error message typically just repeats itself. running the program with gdb gets me: Starting program: /Applications/GRASS-6.4.app/Contents/MacOS/bin/ r.li.patchnum .li.patchnum map=northrast conf=whole out=test Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_INVALID_ADDRESS at address: 0x0008 0x7fff806b0964 in strcmp () and if I backtrace: (gdb) bt #0 0x7fff806b0964 in strcmp () #1 0x00010005bc63 in parseSetup () #2 0x00010005c899 in calculateIndex () #3 0x000108c8 in start () that's as much as I've been able to learn so far given my limited skills at this. On Aug 11, 2009, at 9:00 AM, William Kyngesburye wrote: Here's an interesting clue (or maybe a completely different problem) - our previous crash was run 64bit. When I force the 32bit binary to run with arch -386 (OSX-only command) I still get lots of: WARNING: Unable to open header file for raster map @(null) CHILD[pid = x]: unable to open mask ... continue without!!! but no illegal filename errors and no crash and all the workers processes complete. I don't know what the output is supposed to look like, but the raster looks sensible. I'll try poking around with some debugging. Maybe a bug report is in order also? On Aug 11, 2009, at 12:28 AM, Markus Neteler wrote: On Mon, Aug 10, 2009 at 4:44 PM, Nathan Lemoinelemoine.nat...@gmail.com wrote: I copied landuse96_28m file to the user1 MAPSET (I named the copy landuse), (note that above step isn't really needed, but ok): and used r.li.setup to make my config file. I named the config file mov and selected the landuse raster file. I set the sampling frame to the whole region, and set the sampling area to a moving window. I chose a rectangular window of 5x5 cells. The config file was the set and seemed to be fine. I attempted to run r.li.patchnum rast=landuse config=mov output=test and got the following reports: This is the GRASS terminal report: Illegal filename. Character not allowed. Illegal filename. Character not allowed. ... I have tried: GRASS 6.5.svn (nc_spm_08):~ g.copy rast=landuse96_28m,landuse Copy raster landuse96_...@permanent to current mapset as landuse GRASS 6.5.svn (nc_spm_08):~ g.region rast=landuse GRASS 6.5.svn (nc_spm_08):~ r.li.patchnum landuse96_28m conf=mov output=test --o r.li.worker (pid 29902) terminated r.li.worker (pid 29909) terminated r.li.worker (pid 29910) terminated r.li.worker (pid 29905) terminated r.li.worker (pid 29903) terminated r.li.worker (pid 29908) terminated r.li.worker (pid 29906) terminated r.li.worker (pid 29907) terminated r.li.worker (pid 29904) terminated r.li.worker (pid 29911) terminated Also 6.4: GRASS 6.4.0svn (nc_spm_08):~ r.li.patchnum landuse96_28m conf=mov output=test --o r.li.worker (pid 30035) terminated r.li.worker (pid 30034) terminated r.li.worker (pid 30029) terminated r.li.worker (pid 30030) terminated r.li.worker (pid 30033) terminated r.li.worker (pid 30037) terminated r.li.worker (pid 30038) terminated r.li.worker (pid 30032) terminated r.li.worker (pid 30036) terminated r.li.worker (pid 30031) terminated It works on Linux but apparently the map name gets lost in the r.li daemon on MacOSX. I am afraid that only debugging on Mac helps. The easiest is perhaps to add G_debug() statements if you don't want/cannot use a gdb debugger - to figure out in which code area of r.li.daemon or r.li.patchnum the name disappears. Markus ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - William Kyngesburye kyngchaos*at*kyngchaos*dot*com http://www.kyngchaos.com/ Those people who most want to rule people are, ipso-facto, those least suited to do it. - A rule of the universe, from the HitchHiker's Guide to the Galaxy ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] r.li help
On Mon, Aug 17, 2009 at 2:59 AM, Nathan Lemoinelemoine.nat...@gmail.com wrote: I've tried running gdb on the r.li.patchnum program, but I have no debugging or programming experience, so I can only report the error messages I've received. running the program normally, without of gdb, gets me the error: Illegal filename. Character not allowed. Illegal filename. Character not allowed. Illegal filename. Character not allowed. WARNING: Unable to open header file for raster map @(null) CHILD[pid = 326]: unable to open mask ... continue without!!! this error message typically just repeats itself. Did you compile yourself? If yes, could you update from SVN and recompile r.li*? I added a debug statement which you can activate like this: g.gisenv set=DEBUG=1 Then it should say more about this config file and its path. running the program with gdb gets me: Starting program: /Applications/GRASS-6.4.app/Contents/MacOS/bin/r.li.patchnum .li.patchnum map=northrast conf=whole out=test Program received signal EXC_BAD_ACCESS, Could not access memory. Reason: KERN_INVALID_ADDRESS at address: 0x0008 0x7fff806b0964 in strcmp () and if I backtrace: (gdb) bt #0 0x7fff806b0964 in strcmp () #1 0x00010005bc63 in parseSetup () #2 0x00010005c899 in calculateIndex () #3 0x000108c8 in start () It might come from the conf file not found. that's as much as I've been able to learn so far given my limited skills at this. We are getting closer... :) Markus ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] r.li help
Markus Neteler ha scritto: My result, upper left corner only, is attached (Mandriva Linux, 64bit). Visually it looks ok to me. I'm also having problems with r.li: r.li.shannon map=uso conf=latignano_5 output=provaln WARNING: Unable to open header file for raster map @(null) CHILD[pid = 1954]: unable to open mask ... continue without!!! WARNING: Unable to open header file for raster map @(null) CHILD[pid = 1953]: unable to open mask ... continue without!!! WARNING: Unable to open header file for raster map @(null) CHILD[pid = 1952]: unable to open mask ... continue without!!! WARNING: Unable to open header file for raster map @(null) CHILD[pid = 1951]: unable to open mask ... continue without!!! WARNING: Unable to open header file for raster map @(null) CHILD[pid = 1950]: unable to open mask ... continue without!!! WARNING: Unable to open header file for raster map @(null) CHILD[pid = 1949]: unable to open mask ... continue without!!! WARNING: Unable to open header file for raster map @(null) CHILD[pid = 1948]: unable to open mask ... continue without!!! WARNING: Unable to open header file for raster map @(null) CHILD[pid = 1947]: unable to open mask ... continue without!!! WARNING: Unable to open header file for raster map @(null) CHILD[pid = 1946]: unable to open mask ... continue without!!! WARNING: Unable to open header file for raster map @(null) CHILD[pid = 1945]: unable to open mask ... continue without!!! Segmentation fault Debian ustable, 64 bit. Any hint appreciated. -- Paolo Cavallini: http://www.faunalia.it/pc ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] r.li help
I did a little crude debugging yesterday (G_message) and found it
failed for me in daemon.c, line 626 / nextArea()
else {
return next(g, m);
}
But all this tells me is that at this point the mask name is missing,
not where it was lost.
I didn't have more time to poke around more.
Note: bug report at http://trac.osgeo.org/grass/ticket/718
On Aug 12, 2009, at 9:34 AM, Markus Neteler wrote:
On Wed, Aug 12, 2009 at 3:38 PM, Paolo
Cavallinicavall...@faunalia.it wrote:
Markus Neteler ha scritto:
My result, upper left corner only, is attached (Mandriva Linux,
64bit).
Visually it looks ok to me.
I'm also having problems with r.li:
r.li.shannon map=uso conf=latignano_5 output=provaln
WARNING: Unable to open header file for raster map @(null)
CHILD[pid = 1954]: unable to open mask ... continue without!!!
WARNING: Unable to open header file for raster map @(null)
CHILD[pid = 1953]: unable to open mask ... continue without!!!
WARNING: Unable to open header file for raster map @(null)
CHILD[pid = 1952]: unable to open mask ... continue without!!!
WARNING: Unable to open header file for raster map @(null)
CHILD[pid = 1951]: unable to open mask ... continue without!!!
WARNING: Unable to open header file for raster map @(null)
CHILD[pid = 1950]: unable to open mask ... continue without!!!
WARNING: Unable to open header file for raster map @(null)
CHILD[pid = 1949]: unable to open mask ... continue without!!!
WARNING: Unable to open header file for raster map @(null)
CHILD[pid = 1948]: unable to open mask ... continue without!!!
WARNING: Unable to open header file for raster map @(null)
CHILD[pid = 1947]: unable to open mask ... continue without!!!
WARNING: Unable to open header file for raster map @(null)
CHILD[pid = 1946]: unable to open mask ... continue without!!!
WARNING: Unable to open header file for raster map @(null)
CHILD[pid = 1945]: unable to open mask ... continue without!!!
Segmentation fault
Debian ustable, 64 bit.
Any hint appreciated.
I see three options:
- use the debugger
http://grass.osgeo.org/wiki/GRASS_Debugging#Using_GDB
- otherwise fill the source code with G_debug() statements to figure
out
where it fails (needs recompilation obviously)
- grant access to a machine where it fails, hoping that a GRASS
developers tracks it down for you :)
Markus
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[Trillian] What are you supposed to do WITH a maniacally depressed
robot?
[Marvin] You think you have problems? What are you supposed to do if
you ARE a maniacally depressed robot? No, don't try and answer, I'm
50,000 times more intelligent than you and even I don't know the
answer...
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Re: [GRASS-user] r.li help
Here's an interesting clue (or maybe a completely different problem) - our previous crash was run 64bit. When I force the 32bit binary to run with arch -386 (OSX-only command) I still get lots of: WARNING: Unable to open header file for raster map @(null) CHILD[pid = x]: unable to open mask ... continue without!!! but no illegal filename errors and no crash and all the workers processes complete. I don't know what the output is supposed to look like, but the raster looks sensible. I'll try poking around with some debugging. Maybe a bug report is in order also? On Aug 11, 2009, at 12:28 AM, Markus Neteler wrote: On Mon, Aug 10, 2009 at 4:44 PM, Nathan Lemoinelemoine.nat...@gmail.com wrote: I copied landuse96_28m file to the user1 MAPSET (I named the copy landuse), (note that above step isn't really needed, but ok): and used r.li.setup to make my config file. I named the config file mov and selected the landuse raster file. I set the sampling frame to the whole region, and set the sampling area to a moving window. I chose a rectangular window of 5x5 cells. The config file was the set and seemed to be fine. I attempted to run r.li.patchnum rast=landuse config=mov output=test and got the following reports: This is the GRASS terminal report: Illegal filename. Character not allowed. Illegal filename. Character not allowed. ... I have tried: GRASS 6.5.svn (nc_spm_08):~ g.copy rast=landuse96_28m,landuse Copy raster landuse96_...@permanent to current mapset as landuse GRASS 6.5.svn (nc_spm_08):~ g.region rast=landuse GRASS 6.5.svn (nc_spm_08):~ r.li.patchnum landuse96_28m conf=mov output=test --o r.li.worker (pid 29902) terminated r.li.worker (pid 29909) terminated r.li.worker (pid 29910) terminated r.li.worker (pid 29905) terminated r.li.worker (pid 29903) terminated r.li.worker (pid 29908) terminated r.li.worker (pid 29906) terminated r.li.worker (pid 29907) terminated r.li.worker (pid 29904) terminated r.li.worker (pid 29911) terminated Also 6.4: GRASS 6.4.0svn (nc_spm_08):~ r.li.patchnum landuse96_28m conf=mov output=test --o r.li.worker (pid 30035) terminated r.li.worker (pid 30034) terminated r.li.worker (pid 30029) terminated r.li.worker (pid 30030) terminated r.li.worker (pid 30033) terminated r.li.worker (pid 30037) terminated r.li.worker (pid 30038) terminated r.li.worker (pid 30032) terminated r.li.worker (pid 30036) terminated r.li.worker (pid 30031) terminated It works on Linux but apparently the map name gets lost in the r.li daemon on MacOSX. I am afraid that only debugging on Mac helps. The easiest is perhaps to add G_debug() statements if you don't want/cannot use a gdb debugger - to figure out in which code area of r.li.daemon or r.li.patchnum the name disappears. Markus ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - William Kyngesburye kyngchaos*at*kyngchaos*dot*com http://www.kyngchaos.com/ Those people who most want to rule people are, ipso-facto, those least suited to do it. - A rule of the universe, from the HitchHiker's Guide to the Galaxy ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] r.li help
Markus - I ran patchdensity, here's the upper-left corner of the 32bit run on the spearfish landuse raster, does this look the same as you get? I'm wondering about the overlapping parts, if they should be combined like that (it's working despite the mask errors) or if they should be a single color/value or something else (it's not working)? inline: Picture 1.png On Aug 11, 2009, at 9:00 AM, William Kyngesburye wrote: Here's an interesting clue (or maybe a completely different problem) - our previous crash was run 64bit. When I force the 32bit binary to run with arch -386 (OSX-only command) I still get lots of: WARNING: Unable to open header file for raster map @(null) CHILD[pid = x]: unable to open mask ... continue without!!! but no illegal filename errors and no crash and all the workers processes complete. I don't know what the output is supposed to look like, but the raster looks sensible. I'll try poking around with some debugging. Maybe a bug report is in order also? On Aug 11, 2009, at 12:28 AM, Markus Neteler wrote: On Mon, Aug 10, 2009 at 4:44 PM, Nathan Lemoinelemoine.nat...@gmail.com wrote: I copied landuse96_28m file to the user1 MAPSET (I named the copy landuse), (note that above step isn't really needed, but ok): and used r.li.setup to make my config file. I named the config file mov and selected the landuse raster file. I set the sampling frame to the whole region, and set the sampling area to a moving window. I chose a rectangular window of 5x5 cells. The config file was the set and seemed to be fine. I attempted to run r.li.patchnum rast=landuse config=mov output=test and got the following reports: This is the GRASS terminal report: Illegal filename. Character not allowed. Illegal filename. Character not allowed. ... I have tried: GRASS 6.5.svn (nc_spm_08):~ g.copy rast=landuse96_28m,landuse Copy raster landuse96_...@permanent to current mapset as landuse GRASS 6.5.svn (nc_spm_08):~ g.region rast=landuse GRASS 6.5.svn (nc_spm_08):~ r.li.patchnum landuse96_28m conf=mov output=test --o r.li.worker (pid 29902) terminated r.li.worker (pid 29909) terminated r.li.worker (pid 29910) terminated r.li.worker (pid 29905) terminated r.li.worker (pid 29903) terminated r.li.worker (pid 29908) terminated r.li.worker (pid 29906) terminated r.li.worker (pid 29907) terminated r.li.worker (pid 29904) terminated r.li.worker (pid 29911) terminated Also 6.4: GRASS 6.4.0svn (nc_spm_08):~ r.li.patchnum landuse96_28m conf=mov output=test --o r.li.worker (pid 30035) terminated r.li.worker (pid 30034) terminated r.li.worker (pid 30029) terminated r.li.worker (pid 30030) terminated r.li.worker (pid 30033) terminated r.li.worker (pid 30037) terminated r.li.worker (pid 30038) terminated r.li.worker (pid 30032) terminated r.li.worker (pid 30036) terminated r.li.worker (pid 30031) terminated It works on Linux but apparently the map name gets lost in the r.li daemon on MacOSX. I am afraid that only debugging on Mac helps. The easiest is perhaps to add G_debug() statements if you don't want/cannot use a gdb debugger - to figure out in which code area of r.li.daemon or r.li.patchnum the name disappears. Markus ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - William Kyngesburye kyngchaos*at*kyngchaos*dot*com http://www.kyngchaos.com/ Those people who most want to rule people are, ipso-facto, those least suited to do it. - A rule of the universe, from the HitchHiker's Guide to the Galaxy ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - William Kyngesburye kyngchaos*at*kyngchaos*dot*com http://www.kyngchaos.com/ Time is an illusion - lunchtime doubly so. - Ford Prefect ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] r.li help
On Tue, Aug 11, 2009 at 5:56 PM, William Kyngesburyewokl...@kyngchaos.com wrote: Markus - I ran patchdensity, here's the upper-left corner of the 32bit run on the spearfish landuse raster, does this look the same as you get? I'm wondering about the overlapping parts, if they should be combined like that (it's working despite the mask errors) or if they should be a single color/value or something else (it's not working)? # Spearfish g.region rast=landuse r.li.patchnum map=landuse conf=mov output=test d.mon x0 d.rast landuse d.mon x1 d.rast test My result, upper left corner only, is attached (Mandriva Linux, 64bit). Visually it looks ok to me. Markus attachment: r_li_patchnum.png___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] r.li help
When it crashes, if you get a crash dialog box, click the Report button and copy the details text from that (don't send the crash report). or Run Console.app and look for a crash log for r.li.patchnum in your home Library. On Aug 10, 2009, at 12:43 AM, Nathan Lemoine wrote: I just installed GRASS 6.4 on MacOS X and have been attempting to run some landscape analysis with the r.li modules. I can run the r.li.setup module just fine, but when I attempt to run r.li.patchnum or the density function it just crashes immediately. I've run it from the python GUI and the command-line and the same thing happens. Is there a fix for this? Thanks, Nate ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user - William Kyngesburye kyngchaos*at*kyngchaos*dot*com http://www.kyngchaos.com/ The beast is actively interested only in now, and, as it is always now and always shall be, there is an eternity of time for the accomplishment of objects. - the wisdom of Tarzan ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] r.li help
I've attempted to find the config file on my harddrive and can't seem to locate it. It shows up when I run r.li.setup in the list of available config files and seems to load fine, but when i search for the file it isn't on my harddrive. The config file is supposed to be in the path ~/.r.li/history, but r.li.setup does not create such a path. I've run the r.le.setup which creates the appropriate file path in my user folder to the r.le config files, but r.li does not seem to do this. On Aug 10, 2009, at 12:49 PM, Markus Neteler wrote: Can you please send the config file to me? Markus PS: please keep the list in the loop since other may be able to help even better than me... On Mon, Aug 10, 2009 at 4:44 PM, Nathan Lemoinelemoine.nat...@gmail.com wrote: I copied landuse96_28m file to the user1 MAPSET (I named the copy landuse), and used r.li.setup to make my config file. I named the config file mov and selected the landuse raster file. I set the sampling frame to the whole region, and set the sampling area to a moving window. I chose a rectangular window of 5x5 cells. The config file was the set and seemed to be fine. I attempted to run r.li.patchnum rast=landuse config=mov output=test and got the following reports: This is the GRASS terminal report: Illegal filename. Character not allowed. Illegal filename. Character not allowed. Illegal filename. Character not allowed. Unable to open header file for raster map @(null) CHILD[pid = 1486]: unable to open mask ... continue without!!! Illegal filename. Character not allowed. Illegal filename. Character not allowed. Illegal filename. Character not allowed. Unable to open header file for raster map @(null) CHILD[pid = 1485]: unable to open mask ... continue without!!! and here is the crash report: Process: r.li.patchnum [1476] Path: /Applications/GRASS-6.4.app/Contents/MacOS/bin/r.li.patchnum Identifier: r.li.patchnum Version: ??? (???) Code Type: X86-64 (Native) Parent Process: Python [981] Interval Since Last Report: 134 sec Crashes Since Last Report: 5 Per-App Interval Since Last Report: 0 sec Per-App Crashes Since Last Report: 5 Date/Time: 2009-08-10 09:40:14.814 -0500 OS Version: Mac OS X 10.5.8 (9L30) Report Version: 6 Anonymous UUID: 79A157D4-B61F-432E-8CB4-A2211DE1A30D Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x006174614420 Crashed Thread: 0 Thread 0 Crashed: 0 libSystem.B.dylib 0x7fff806cfd70 strcpy + 48 1 libgrass_rli.dylib 0x00010005c3ed next_Area + 111 2 libgrass_rli.dylib 0x00010005ca8a calculateIndex + 859 3 r.li.patchnum 0x000108c8 start + 52 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0005 rbx: 0x7fff5fbfe600 rcx: 0x7fff5fbfe4fc rdx: 0x0004 rdi: 0x7fff5fbfe4fc rsi: 0x006174614420 rbp: 0x7fff5fbfaea0 rsp: 0x7fff5fbfae98 r8: 0x0001001fe026 r9: 0x0208 r10: 0x0001000618c0 r11: 0x7fff806cfd40 r12: 0x0001001007d0 r13: 0x7fff5fbfe4e0 r14: 0x0001001007d0 r15: 0x rip: 0x7fff806cfd70 rfl: 0x00010202 cr2: 0x006174614420 Binary Images: 0x1 -0x10fff +r.li.patchnum ??? (???) 06f892abad9a2d2989b9c21d1b12d783 /Applications/GRASS-6.4.app/Contents/MacOS/bin/r.li.patchnum 0x13000 -0x100041ff7 +libgrass_gis.dylib ??? (???) 3f754d3fd572946f5f5c57939c5efd58 /Applications/GRASS-6.4.app/Contents/MacOS/lib/libgrass_gis.dylib 0x100052000 -0x100057fff +libgrass_datetime.dylib ??? (???) 366b12b0e9b5622047457160897ad0ee /Applications/GRASS-6.4.app/Contents/MacOS/lib/ libgrass_datetime.dylib 0x10005a000 -0x10005 +libgrass_rli.dylib ??? (???) d5dd64d7346e0357e77ecc2d883b4bd0 /Applications/GRASS-6.4.app/Contents/MacOS/lib/libgrass_rli.dylib 0x7fff5fc0 - 0x7fff5fc2e643 dyld 97.1 (???) 1d1ba42c89e77cfe2558a3c66129fff6 /usr/lib/dyld 0x7fff806a7000 - 0x7fff80832ffb libSystem.B.dylib ??? (???) 714d2608b5acae3ad5364897c49868fa /usr/lib/libSystem.B.dylib 0x7fff81d78000 - 0x7fff81d89ffd libz.1.dylib ??? (???) 2022cc8950afdf485ba1df76364ba725 /usr/lib/libz.1.dylib 0x7fff82abc000 - 0x7fff82ac8ff1 libgcc_s.1.dylib ??? (???) 6fc905606335f261db4da9529c7e2711 /usr/lib/libgcc_s.1.dylib 0x7fff841fd000 - 0x7fff84201fff libmathCommon.A.dylib ??? (???) /usr/lib/system/libmathCommon.A.dylib 0x7fe0 - 0x7fe01780 libSystem.B.dylib ??? (???) /usr/lib/libSystem.B.dylib This seems to be a different issue than when I attempted it with my own data, but I'm still looking into that. Nate On Aug 10, 2009, at 1:20 AM, Markus Neteler wrote: On Mon, Aug 10, 2009 at 7:43 AM, Nathan Lemoinelemoine.nat...@gmail.com wrote:
Re: [GRASS-user] r.li help
On Mon, Aug 10, 2009 at 8:20 PM, Nathan Lemoinelemoine.nat...@gmail.com wrote: I've attempted to find the config file on my harddrive and can't seem to locate it. It shows up when I run r.li.setup in the list of available config files and seems to load fine, but when i search for the file it isn't on my harddrive. The config file is supposed to be in the path ~/.r.li/history, but r.li.setup does not create such a path. Then that's perhaps the problem? William, does it create on your Mac the directory? Markus I've run the r.le.setup which creates the appropriate file path in my user folder to the r.le config files, but r.li does not seem to do this. On Aug 10, 2009, at 12:49 PM, Markus Neteler wrote: Can you please send the config file to me? Markus PS: please keep the list in the loop since other may be able to help even better than me... On Mon, Aug 10, 2009 at 4:44 PM, Nathan Lemoinelemoine.nat...@gmail.com wrote: I copied landuse96_28m file to the user1 MAPSET (I named the copy landuse), and used r.li.setup to make my config file. I named the config file mov and selected the landuse raster file. I set the sampling frame to the whole region, and set the sampling area to a moving window. I chose a rectangular window of 5x5 cells. The config file was the set and seemed to be fine. I attempted to run r.li.patchnum rast=landuse config=mov output=test and got the following reports: This is the GRASS terminal report: Illegal filename. Character not allowed. Illegal filename. Character not allowed. Illegal filename. Character not allowed. Unable to open header file for raster map @(null) CHILD[pid = 1486]: unable to open mask ... continue without!!! Illegal filename. Character not allowed. Illegal filename. Character not allowed. Illegal filename. Character not allowed. Unable to open header file for raster map @(null) CHILD[pid = 1485]: unable to open mask ... continue without!!! and here is the crash report: Process: r.li.patchnum [1476] Path: /Applications/GRASS-6.4.app/Contents/MacOS/bin/r.li.patchnum Identifier: r.li.patchnum Version: ??? (???) Code Type: X86-64 (Native) Parent Process: Python [981] Interval Since Last Report: 134 sec Crashes Since Last Report: 5 Per-App Interval Since Last Report: 0 sec Per-App Crashes Since Last Report: 5 Date/Time: 2009-08-10 09:40:14.814 -0500 OS Version: Mac OS X 10.5.8 (9L30) Report Version: 6 Anonymous UUID: 79A157D4-B61F-432E-8CB4-A2211DE1A30D Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x006174614420 Crashed Thread: 0 Thread 0 Crashed: 0 libSystem.B.dylib 0x7fff806cfd70 strcpy + 48 1 libgrass_rli.dylib 0x00010005c3ed next_Area + 111 2 libgrass_rli.dylib 0x00010005ca8a calculateIndex + 859 3 r.li.patchnum 0x000108c8 start + 52 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x0005 rbx: 0x7fff5fbfe600 rcx: 0x7fff5fbfe4fc rdx: 0x0004 rdi: 0x7fff5fbfe4fc rsi: 0x006174614420 rbp: 0x7fff5fbfaea0 rsp: 0x7fff5fbfae98 r8: 0x0001001fe026 r9: 0x0208 r10: 0x0001000618c0 r11: 0x7fff806cfd40 r12: 0x0001001007d0 r13: 0x7fff5fbfe4e0 r14: 0x0001001007d0 r15: 0x rip: 0x7fff806cfd70 rfl: 0x00010202 cr2: 0x006174614420 Binary Images: 0x1 - 0x10fff +r.li.patchnum ??? (???) 06f892abad9a2d2989b9c21d1b12d783 /Applications/GRASS-6.4.app/Contents/MacOS/bin/r.li.patchnum 0x13000 - 0x100041ff7 +libgrass_gis.dylib ??? (???) 3f754d3fd572946f5f5c57939c5efd58 /Applications/GRASS-6.4.app/Contents/MacOS/lib/libgrass_gis.dylib 0x100052000 - 0x100057fff +libgrass_datetime.dylib ??? (???) 366b12b0e9b5622047457160897ad0ee /Applications/GRASS-6.4.app/Contents/MacOS/lib/libgrass_datetime.dylib 0x10005a000 - 0x10005 +libgrass_rli.dylib ??? (???) d5dd64d7346e0357e77ecc2d883b4bd0 /Applications/GRASS-6.4.app/Contents/MacOS/lib/libgrass_rli.dylib 0x7fff5fc0 - 0x7fff5fc2e643 dyld 97.1 (???) 1d1ba42c89e77cfe2558a3c66129fff6 /usr/lib/dyld 0x7fff806a7000 - 0x7fff80832ffb libSystem.B.dylib ??? (???) 714d2608b5acae3ad5364897c49868fa /usr/lib/libSystem.B.dylib 0x7fff81d78000 - 0x7fff81d89ffd libz.1.dylib ??? (???) 2022cc8950afdf485ba1df76364ba725 /usr/lib/libz.1.dylib 0x7fff82abc000 - 0x7fff82ac8ff1 libgcc_s.1.dylib ??? (???) 6fc905606335f261db4da9529c7e2711 /usr/lib/libgcc_s.1.dylib 0x7fff841fd000 - 0x7fff84201fff libmathCommon.A.dylib ??? (???) /usr/lib/system/libmathCommon.A.dylib 0x7fe0 - 0x7fe01780 libSystem.B.dylib ??? (???) /usr/lib/libSystem.B.dylib This seems to be a different issue than when I
Re: [GRASS-user] r.li help
On Aug 10, 2009, at 1:44 PM, Markus Neteler wrote: On Mon, Aug 10, 2009 at 8:20 PM, Nathan Lemoinelemoine.nat...@gmail.com wrote: I've attempted to find the config file on my harddrive and can't seem to locate it. It shows up when I run r.li.setup in the list of available config files and seems to load fine, but when i search for the file it isn't on my harddrive. The config file is supposed to be in the path ~/.r.li/ history, but r.li.setup does not create such a path. Then that's perhaps the problem? William, does it create on your Mac the directory? Yes, ~/.r.li/history was created for me. And my test config. It looks sensible: SAMPLINGFRAME 0|0|1|1 SAMPLEAREA -1|-1|0.03571428571428571|0.02631578947368421 MOVINGWINDOW When I ran r.li.patchdensity, I got the segfault (same output and crash log). Markus I've run the r.le.setup which creates the appropriate file path in my user folder to the r.le config files, but r.li does not seem to do this. On Aug 10, 2009, at 12:49 PM, Markus Neteler wrote: Can you please send the config file to me? Markus PS: please keep the list in the loop since other may be able to help even better than me... On Mon, Aug 10, 2009 at 4:44 PM, Nathan Lemoinelemoine.nat...@gmail.com wrote: I copied landuse96_28m file to the user1 MAPSET (I named the copy landuse), and used r.li.setup to make my config file. I named the config file mov and selected the landuse raster file. I set the sampling frame to the whole region, and set the sampling area to a moving window. I chose a rectangular window of 5x5 cells. The config file was the set and seemed to be fine. I attempted to run r.li.patchnum rast=landuse config=mov output=test and got the following reports: - William Kyngesburye kyngchaos*at*kyngchaos*dot*com http://www.kyngchaos.com/ All generalizations are dangerous, even this one. ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
Re: [GRASS-user] r.li help
On Mon, Aug 10, 2009 at 4:44 PM, Nathan Lemoinelemoine.nat...@gmail.com wrote: I copied landuse96_28m file to the user1 MAPSET (I named the copy landuse), (note that above step isn't really needed, but ok): and used r.li.setup to make my config file. I named the config file mov and selected the landuse raster file. I set the sampling frame to the whole region, and set the sampling area to a moving window. I chose a rectangular window of 5x5 cells. The config file was the set and seemed to be fine. I attempted to run r.li.patchnum rast=landuse config=mov output=test and got the following reports: This is the GRASS terminal report: Illegal filename. Character not allowed. Illegal filename. Character not allowed. ... I have tried: GRASS 6.5.svn (nc_spm_08):~ g.copy rast=landuse96_28m,landuse Copy raster landuse96_...@permanent to current mapset as landuse GRASS 6.5.svn (nc_spm_08):~ g.region rast=landuse GRASS 6.5.svn (nc_spm_08):~ r.li.patchnum landuse96_28m conf=mov output=test --o r.li.worker (pid 29902) terminated r.li.worker (pid 29909) terminated r.li.worker (pid 29910) terminated r.li.worker (pid 29905) terminated r.li.worker (pid 29903) terminated r.li.worker (pid 29908) terminated r.li.worker (pid 29906) terminated r.li.worker (pid 29907) terminated r.li.worker (pid 29904) terminated r.li.worker (pid 29911) terminated Also 6.4: GRASS 6.4.0svn (nc_spm_08):~ r.li.patchnum landuse96_28m conf=mov output=test --o r.li.worker (pid 30035) terminated r.li.worker (pid 30034) terminated r.li.worker (pid 30029) terminated r.li.worker (pid 30030) terminated r.li.worker (pid 30033) terminated r.li.worker (pid 30037) terminated r.li.worker (pid 30038) terminated r.li.worker (pid 30032) terminated r.li.worker (pid 30036) terminated r.li.worker (pid 30031) terminated It works on Linux but apparently the map name gets lost in the r.li daemon on MacOSX. I am afraid that only debugging on Mac helps. The easiest is perhaps to add G_debug() statements if you don't want/cannot use a gdb debugger - to figure out in which code area of r.li.daemon or r.li.patchnum the name disappears. Markus ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
[GRASS-user] r.li help
I just installed GRASS 6.4 on MacOS X and have been attempting to run some landscape analysis with the r.li modules. I can run the r.li.setup module just fine, but when I attempt to run r.li.patchnum or the density function it just crashes immediately. I've run it from the python GUI and the command-line and the same thing happens. Is there a fix for this? Thanks, Nate ___ grass-user mailing list grass-user@lists.osgeo.org http://lists.osgeo.org/mailman/listinfo/grass-user
