[GRASS-dev] [GRASS GIS] #3213: v.net.iso - Segmentation fault

GDAL · November 25, 2016, 11:05am

#3213: v.net.iso - Segmentation fault
----------------------+---------------------------------
Reporter: sebastic | Owner: grass-dev@…
Type: defect | Status: new
Priority: normal | Milestone: 7.2.0
Component: Vector | Version: svn-releasebranch72
Keywords: | CPU: Unspecified
Platform: Linux |
----------------------+---------------------------------
As reported by Eduardo Corbelle Rico in [https://bugs.debian.org/845429
Debian Bug #845429]:
> It happened to me that the use of v.net.iso command results in a
> segmentation fault. I could replicate the error in two different
> machines, with my own data and with both examples shown in the online
> manual ( https://grass.osgeo.org/grass70/manuals/v.net.iso.html )
> using the Spearfish dataset for GRASS 7.
>
> After consultation in the GRASS-user list, it seems that this is
> specific of the pre-compiled package (installed via apt-get), as the
> error does not appear when GRASS 7.0 is compiled from source in the
> same machine.

The related discussion on grass-user is at:

https://lists.osgeo.org/pipermail/grass-user/2016-November/075606.html

Running the commands from the example gets the following backtrace from
gdb:
{{{
(gdb) run
Starting program: /usr/lib/grass72/bin/v.net.iso input=myroads_net
output=myroads_net_iso center_cats=1-100000 costs=1000,2000,5000
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
Building graph...
Registering arcs...

Program received signal SIGSEGV, Segmentation fault.
tavl_probe (tree=tree@entry=0x6427d0, item=item@entry=0x84cd30) at
tavl.c:146
146 tavl.c: No such file or directory.
(gdb) bt
#0 tavl_probe (tree=tree@entry=0x6427d0, item=item@entry=0x84cd30) at
tavl.c:146
#1 0x00007ffff6c55737 in dglTreeNodeAdd (pavl=0x6427d0,
nKey=nKey@entry=1) at tree.c:73
#2 0x00007ffff6c4aa0c in dgl_add_edge_V1 (pgraph=0x7fffffffd3a8,
nHead=<optimized out>, nTail=<optimized out>, nCost=1231014, nEdge=1,
pvHeadAttr=pvHeadAttr@entry=0x0, pvTailAttr=0x0, pvEdgeAttr=0x0, nFlags=0)
at edgemgmt-template.c:59
#3 0x00007ffff6c48a62 in dglAddEdge (pGraph=pGraph@entry=0x7fffffffd3a8,
nHead=<optimized out>, nTail=<optimized out>, nCost=<optimized out>,
nEdge=nEdge@entry=1) at graph.c:624
#4 0x00007ffff7ba1769 in Vect_net_build_graph
(Map=Map@entry=0x7fffffffcfd0, ltype=ltype@entry=6, afield=afield@entry=1,
nfield=nfield@entry=2, afcol=0x0, abcol=0x0, ncol=0x0, geo=0, version=1)
at net_build.c:918
#5 0x0000000000402aee in main (argc=<optimized out>, argv=<optimized
out>) at main.c:224
}}}

The issue can be reproduced with the GRASS 7.0.5 and 7.2.0-RC2 packages in
Debian. In what way the custom compile differs from the Debian package
build is not clear yet.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3213>
GRASS GIS <https://grass.osgeo.org>

GDAL · November 28, 2016, 8:42am

#3213: v.net.iso - Segmentation fault
--------------------------+---------------------------------
  Reporter: sebastic | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: major | Milestone: 7.2.0
Component: LibVector | Version: svn-releasebranch72
Resolution: | Keywords:
       CPU: Unspecified | Platform: Linux
--------------------------+---------------------------------
Changes (by mmetz):

* priority: normal => major
* component: Vector => LibVector

Comment:

Adding the full gdb backtrace for reference:

{{{
(gdb) bt full
#0 tavl_probe (tree=tree@entry=0x55555599b6c0, item=item@entry=0x55555
599f7b0)
     at tavl.c:146
         y = 0x0
         z = 0x55555599b6c0
         p = 0x0
         q = <optimized out>
         n = 0x55555599f7d0
         w = <optimized out>
         dir = <optimized out>
         da =
"\023\000\000\000\000\000\000\000\000\vb\367\377\177\000\000\300\266\23
1UUU\000\000\030\000\000\000\000\000\000"
         k = 0
         __PRETTY_FUNCTION__ = "tavl_probe"
}}}

The problem is that y = NULL. The test in tavl.c:139 should have been
positive (new empty tree, the root must be set to the new node).

With regard to lib/vector/dglib, the source code of the Debian package
seems to be identical to svn source code. Therefore, as long as manual
compilation from source works, it seems that this is a packaging error.
FWIW, I have updated tavl.c in trunk r69935 (newer version, more safety
checks).

For debugging purposes, is there any way to reproduce compilation of the
Debian package? It would be really nice to have a working Debian package.
Increasing priority.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3213#comment:1>
GRASS GIS <https://grass.osgeo.org>

GDAL · November 28, 2016, 8:56am

#3213: v.net.iso - Segmentation fault
--------------------------+---------------------------------
  Reporter: sebastic | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: major | Milestone: 7.2.0
Component: LibVector | Version: svn-releasebranch72
Resolution: | Keywords:
       CPU: Unspecified | Platform: Linux
--------------------------+---------------------------------

Comment (by sebastic):

Replying to [comment:1 mmetz]:
> For debugging purposes, is there any way to reproduce compilation of the
Debian package?

Yes, download the source package and build in a Debian unstable chroot
with pdebuild. Or use the package git repository and the git-buildpackage
workflow documented in the Debian GIS Policy:

https://pkg-grass.alioth.debian.org/policy/packaging.html#git-packaging

Look at the debian/rules file for the configure options, and the build log
or dpkg-buildflags for the build flags (CFLAGS, LDFLAGS, etc).

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3213#comment:2>
GRASS GIS <https://grass.osgeo.org>

GDAL · November 29, 2016, 1:40pm

#3213: v.net.iso - Segmentation fault
--------------------------+---------------------------------
  Reporter: sebastic | Owner: grass-dev@…
      Type: defect | Status: new
  Priority: major | Milestone: 7.2.0
Component: LibVector | Version: svn-releasebranch72
Resolution: | Keywords:
       CPU: Unspecified | Platform: Linux
--------------------------+---------------------------------

Comment (by mmetz):

Replying to [comment:2 sebastic]:
> Replying to [comment:1 mmetz]:
> > For debugging purposes, is there any way to reproduce compilation of
the Debian package?
>
> Yes, download the source package and build in a Debian unstable chroot
with pdebuild. Or use the package git repository and the git-buildpackage
workflow documented in the Debian GIS Policy:
>
> https://pkg-grass.alioth.debian.org/policy/packaging.html#git-packaging
>
> Look at the debian/rules file for the configure options, and the build
log or dpkg-buildflags for the build flags (CFLAGS, LDFLAGS, etc).

Thanks. With Debian testing and GRASS 7.0.5, I could reproduce the
segfault with the standard grass package, a rebuilt package, and also
GRASS 7.0.5 compiled from source. Using the new tavl version from trunk
solved the problem. Backported to G72 and G70 in r69951,2.

This code has been working fine for the last 14 years, therefore I am not
sure if it is a bug in the code or a bug in Debian testing/unstable.

The ticket can be closed when new versions of G70 and G72 have been
packaged for Debian and are confirmed working.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3213#comment:3>
GRASS GIS <https://grass.osgeo.org>

GDAL · December 2, 2016, 12:10pm

#3213: v.net.iso - Segmentation fault
--------------------------+---------------------------------
  Reporter: sebastic | Owner: grass-dev@…
      Type: defect | Status: closed
  Priority: major | Milestone: 7.2.0
Component: LibVector | Version: svn-releasebranch72
Resolution: fixed | Keywords:
       CPU: Unspecified | Platform: Linux
--------------------------+---------------------------------
Changes (by sebastic):

* status: new => closed
* resolution: => fixed

Comment:

Confirmed fixed with the changes from r69951 which have been included as a
patch in the Debian package.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3213#comment:4>
GRASS GIS <https://grass.osgeo.org>

GDAL · December 2, 2016, 9:49pm

#3213: v.net.iso - Segmentation fault
--------------------------+---------------------------------
  Reporter: sebastic | Owner: grass-dev@…
      Type: defect | Status: closed
  Priority: major | Milestone: 7.2.0
Component: LibVector | Version: svn-releasebranch72
Resolution: fixed | Keywords:
       CPU: Unspecified | Platform: Linux
--------------------------+---------------------------------

Comment (by mmetz):

Replying to [comment:4 sebastic]:
> Confirmed fixed with the changes from r69951 which have been included as
a patch in the Debian package.

Thanks a lot for patching, testing, and publishing the patched Debian
packages for GRASS 7 so fast!

Maybe related:

There seems to be a problem with the interpretation of C language
standards in Debian testing:

GRASS 7.0.5 does not compile with -std=c99 because math.h is not included
(early error in lib/gis), even though math.h conforms to ISO C99 Standard:
7.12 Mathematics and is included if `__USE_ISOC99` is defined.

GRASS 7.0.5 does compile with -std=gnu99 (C99 with GNU extensions).

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3213#comment:5>
GRASS GIS <https://grass.osgeo.org>

GDAL · December 3, 2016, 10:19am

#3213: v.net.iso - Segmentation fault
--------------------------+---------------------------------
  Reporter: sebastic | Owner: grass-dev@…
      Type: defect | Status: closed
  Priority: major | Milestone: 7.2.0
Component: LibVector | Version: svn-releasebranch72
Resolution: fixed | Keywords:
       CPU: Unspecified | Platform: Linux
--------------------------+---------------------------------

Comment (by sebastic):

Replying to [comment:5 mmetz]:
> GRASS 7.0.5 does not compile with -std=c99 because math.h is not
included (early error in lib/gis), even though math.h conforms to ISO C99
Standard: 7.12 Mathematics and is included if `__USE_ISOC99` is defined.
>
> GRASS 7.0.5 does compile with -std=gnu99 (C99 with GNU extensions).

If GRASS should be compiled with `-std=c99` or `-std=gnu99` the configure
script in GRASS should set these flags when appropriate.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3213#comment:6>
GRASS GIS <https://grass.osgeo.org>

GDAL · December 20, 2016, 9:18am

#3213: v.net.iso - Segmentation fault
--------------------------+---------------------------------
  Reporter: sebastic | Owner: grass-dev@…
      Type: defect | Status: closed
  Priority: major | Milestone: 7.2.0
Component: LibVector | Version: svn-releasebranch72
Resolution: fixed | Keywords:
       CPU: Unspecified | Platform: Linux
--------------------------+---------------------------------

Comment (by mmetz):

Replying to [comment:4 sebastic]:
> Confirmed fixed with the changes from r69951 which have been included as
a patch in the Debian package.

For the record: the exact same segfault happens with Fedora 25 and with
RHEL 7 + devtoolset-6. All use gcc-6.2.

--
Ticket URL: <https://trac.osgeo.org/grass/ticket/3213#comment:7>
GRASS GIS <https://grass.osgeo.org>