Bug #968
-JPr malloc crash on OSX w/ grdcontour and on Linux w/ grdimage
| Status: | Closed | Start date: | 2016-09-21 | |
|---|---|---|---|---|
| Priority: | Normal | Due date: | ||
| Assignee: |  Paul | % Done: | 100% | |
| Category: | - | |||
| Target version: | Candidate for next bugfix release | |||
| Affected version: | 5.2-svn | Platform: | Mac OS X |
Description
Dear GMT team,
referring to the entry in the gmt-user forum (where the full script and data are to find)
[[http://gmt.soest.hawaii.edu/boards/1/topics/4103]]
I file a bug issue for grdcontour and the polar projection (-JP). The nasty command line
gmt grdcontour brdf_14/01_brdf.ring.755.00.ps.dat.nc -JP6ir -Xa2c -Ya4c -By30 -Bx30 -Cbrdf_14/01_brdf.ring.755.00.ps.dat.cpt -A- -W+1p -V -K -O >> brdf_14/01_brdf.ring.755.00.ps.dat.ps
crashes on a Intel Mac OSX 10.11.6 (15G31) with GMT 5.2.1 (r15220) (via MacPorts) with
grdcontour: Processing input grid
grdcontour: Allocate memory and read data file
gmt(48322,0x7fff772a9000) malloc: *** error for object 0x7ff831059608: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
./do-gmt.sh: line 62: 48322 Abort trap: 6 gmt grdcontour $NC ${PROJ} $OFF $AXy $AXx $FORMAT -C$COL -A- $CONT -V -K -O >> $PLOT
ERROR: Caught signal number 11 (Segmentation fault) at
0 libsystem_malloc.dylib 0x00007fff9158beec small_malloc_from_free_list + 584
1 ??? 0x0000000000000000 0x0 + 0
Stack backtrace:
0 libgmt.5.dylib 0x000000010c6eecd2 sig_handler + 338
1 libsystem_platform.dylib 0x00007fff987a252a _sigtramp + 26
2 ??? 0x00007fff5351ca20 0x0 + 140734591257120
3 libsystem_malloc.dylib 0x00007fff91588b64 szone_malloc_should_clear + 1411
4 libsystem_malloc.dylib 0x00007fff9158b9a6 malloc_zone_calloc + 78
5 libsystem_malloc.dylib 0x00007fff9158c462 calloc + 49
6 libpostscriptlight.5.dylib 0x0000000110e6a2f2 PSL_plotline + 66
7 libpostscriptlight.5.dylib 0x0000000110e6a212 PSL_beginclipping + 98
8 libgmt.5.dylib 0x000000010c810b2c GMT_map_clip_on + 172
9 libgmt.5.dylib 0x000000010c93da55 GMT_grdcontour + 9013
10 libgmt.5.dylib 0x000000010c70346c GMT_Call_Module + 284
11 gmt 0x000000010c6e6307 main + 1159
12 libdyld.dylib 0x00007fff911765ad start + 1
13 ??? 0x000000000000000c 0x0 + 12
Consistently but more interestingly the almost same behaviour with the same script is obtained on a Linux installation with the combination of
Linux 3.13.0-86-generic #131-Ubuntu x86_64 GNU/Linux
gmt --version 5.1.2 (r14084)
but now the script crashes already with grdimage as
grdimage: Allocates memory and read data file
*** Error in `gmt': malloc(): memory corruption: 0x0000000001f8dc30 ***
./do-gmt.sh: line 87: 14867 Aborted (core dumped) gmt grdimage $NC $PROJ $OFF -C$COL -K -V > $PLOT
gmt grdcontour brdf_14/brdf.ring.758.00.ps.dat.nc -JP15.24cr -Xa2c -Ya4c -By30 -Bx30 -Cbrdf_14/brdf.ring.758.00.ps.dat.cpt -A- -W+1p -V -K -O >> brdf_14/brdf.ring.758.00.ps.dat.ps
*** Error in `gmt': malloc(): memory corruption: 0x0000000001d81940 ***
./do-gmt.sh: line 93: 14869 Aborted (core dumped) gmt grdcontour $NC ${PROJ} $OFF $AXy $AXx $FORMAT -C$COL -A- $CONT -K -O >> $PLOT
*** Error in `gmt': malloc(): memory corruption: 0x0000000000af2ce0 ***
./do-gmt.sh: line 96: 14871 Aborted (core dumped) gmt grdcontour $ANGLENC $PROJ $OFF -Gd5c -C10 $CONTb -A20+f22.5+u'\260' -K -O >> $PLOT
Regards
do-gmt-polar.sh 
(1.45 KB)
test.dat.wrong.png (29.1 KB)
test.dat.correct.png (64.6 KB)
test.dat (44 KB)
test.dat.linux.wrong.png (17.8 KB)
Associated revisions
Add two test derived from issue #968
History
Updated by 
#2
Updated by Luca 10 months ago
- File test.dat.correct.png added
- File do-gmt-polar.sh added
- File test.dat.wrong.png added
- File test.dat added
Joaquim wrote:
Luca, the problem is that with this information we are not able to try to reproduce the issue.
We also need the input data (or a small subset that allows to reproduce the problem).
Hello Joaquim, thanks for the reply.
I'm attaching 4 files: the script, the test data, the correct output plot (obtained with -JP6i) and the wrong output plot (with -JP6ir).
This happens for the Intel Mac OSX 10.11.6 (15G31) with GMT 5.2.1 (r15220) (via MacPorts).
The error message reads:
grdcontour: Processing input grid
grdcontour: Allocate memory and read data file
gmt(15967,0x7fff7bf76000) malloc: *** error for object 0x7fae84865a08: incorrect checksum for freed object - object was probably modified after being freed.
*** set a breakpoint in malloc_error_break to debug
./do-gmt-polar.sh: line 39: 15967 Abort trap: 6 gmt grdcontour $NC ${PROJ} $OFF $AXy $AXx $FORMAT -C$COL -A- $CONT -V -K -O >> $PLOT
Hope you can reproduce the behaviour.
Regards.
#5
Updated by Luca 10 months ago
- File test.dat.linux.wrong.png added
Joaquim wrote:
Correction, yes I can reproduce it. It's that I just run your script and that worked but if I add the 'r' to the projection than it crashes.
Thanks Joaquim.
If it may help, I was experimenting with the development subversion ( 5.3.0_r17114 ) on the Linux box instead, and I get the same error message
grdimage: Allocates memory and read data file
*** Error in `gmt': malloc(): memory corruption: 0x0000000000853770 ***
./do-gmt-polar.sh: line 35: 2011 Aborted (core dumped) gmt grdimage $NC $PROJ $OFF -C$COL -V -K > $PLOT
grdcontour: Processing input grid
grdcontour: Allocate memory and read data file
*** Error in `gmt': malloc(): memory corruption: 0x00000000025fbd60 ***
./do-gmt-polar.sh: line 39: 2013 Aborted (core dumped) gmt grdcontour $NC ${PROJ} $OFF $AXy $AXx $FORMAT -C$COL -A- $CONT -V -K -O >> $PLOT
but now with a different wrong output plot (attached).
Regards
#7
Updated by Paul 10 months ago
- Status changed from In Progress to Resolved
- Assignee set to Paul
We had an allocation problem where one test said we needed N points and then the calculation needed 2*N points. Should be fixed in r17145 - let us know. We added a couple of tests to the test suite inspired by your script and they pass.