Details Ticket 4349


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Serial Number 4349
Subject Segfault in several display modules on x86_64
Area grass6
Queue grass
Requestors SorokinA@ornl.gov
Owner none
Status resolved
Last User Contact Sun Apr 30 21:34:45 2006 (2 yr ago)
Current Priority 70
Final Priority 70
Due No date assigned
Last Action Wed May 3 08:28:01 2006 (2 yr ago)
Created Wed Apr 26 22:41:43 2006 (2 yr ago)

Transaction History Ticket 4349


Wed, Apr 26 2006 22:41:43    Request created by guest  
Subject: Segfault in several display modules on x86_64 

Platform: GNU/Linux/x86_64
grass binary for platform: Compiled from Sources
GRASS Version: GRASS 6.1.cvs (2006) checkout 4/22/06

Segfault in several display modules (d.vect, d.zoom) on x86_64, Suse 9.2.  
uname -a:

Linux node0 2.6.5-7.244_lustre.1.4.6smp #1 SMP Sat Feb 18 17:33:39 EST 2006 x86_64
x86_64 x86_64 GNU/Linux

For both d.vect and d.zoom SIGSEGV can be traced to G_whoami () at whoami.c:64.
Here is GDB stack trace:

(gdb) where
#0  0x0000002a96a33915 in strcpy () from /lib64/tls/libc.so.6
#1  0x0000002a95ef7ecc in set_string (x=0x50c4bc, s=0x2a95dec773 "0", copy=1)
at string.c:108
#2  0x0000002a95deb05b in db_version (driver=0x50c4b8,
    client_version=0x50c4bc, driver_version=0x50c4c0) at c_version.c:20
#3  0x0000002a97be6a01 in __db_e_attach () from /usr/lib64/tls/libdb-4.2.so
#4  0x0000002a97be4759 in __dbenv_open () from /usr/lib64/tls/libdb-4.2.so
#5  0x0000002a97bc146e in __db_dbenv_setup () from /usr/lib64/tls/libdb-4.2.so
#6  0x0000002a97bd5e6a in __db_open () from /usr/lib64/tls/libdb-4.2.so
#7  0x0000002a97bd0c4d in __db_open_pp () from /usr/lib64/tls/libdb-4.2.so
#8  0x0000002a97b707ea in __db185_open () from /usr/lib64/tls/libdb-4.2.so
#9  0x0000002a977fcf5d in _nss_hash_open () from /lib64/libnss_ldap.so.2
#10 0x0000002a977fd0b5 in _nss_ldap_init_config () from /lib64/libnss_ldap.so.2
#11 0x0000002a977fd149 in _nss_ldap_readconfig () from /lib64/libnss_ldap.so.2
#12 0x0000002a977f7b21 in do_open () from /lib64/libnss_ldap.so.2
#13 0x0000002a977f84c0 in _nss_ldap_search_s () from /lib64/libnss_ldap.so.2
#14 0x0000002a977f8a48 in _nss_ldap_getbyname () from /lib64/libnss_ldap.so.2
#15 0x0000002a977f9300 in _nss_ldap_getpwuid_r () from /lib64/libnss_ldap.so.2
#16 0x0000002a96a5290d in getpwuid_r@@GLIBC_2.2.5 () from /lib64/tls/libc.so.6
#17 0x0000002a96a5228d in getpwuid () from /lib64/tls/libc.so.6
#18 0x0000002a964c3f35 in G_whoami () at whoami.c:64
#19 0x0000002a964c22f3 in G_sock_get_fname (name=0x507470 "x0")
    at unix_socks.c:68
#20 0x0000002a9577c4b1 in R_open_driver () at io_sock.c:73
#21 0x0000000000402c98 in main (argc=1, argv=0x7fbfffea78) at main.c:47
Wed, Apr 26 2006 22:43:15    Comments added by guest  
gdb trace is for d.zoom
Thu, Apr 27 2006 18:24:25    Mail sent by glynn@gclements.plus.com  
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From Glynn Clements <glynn@gclements.plus.com>
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Date Thu, 27 Apr 2006 17:24:19 +0100
To Request Tracker <grass-bugs@intevation.de>
Cc grass5@grass.itc.it
Subject Re: [GRASS5] [bug #4349] (grass) Segfault in several display modules on x86_64
In-Reply-To <20060426204143.E1BC41005CD@lists.intevation.de>
References <20060426204143.E1BC41005CD@lists.intevation.de>
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Request Tracker wrote:

> this bug's URL: http://intevation.de/rt/webrt?serial_num=4349
> -------------------------------------------------------------------------
> 
> Subject: Segfault in several display modules on x86_64 
> 
> Platform: GNU/Linux/x86_64
> grass binary for platform: Compiled from Sources
> GRASS Version: GRASS 6.1.cvs (2006) checkout 4/22/06
> 
> Segfault in several display modules (d.vect, d.zoom) on x86_64, Suse 9.2. 
> 
> uname -a:
> 
> Linux node0 2.6.5-7.244_lustre.1.4.6smp #1 SMP Sat Feb 18 17:33:39 EST 2006
x86_64 x86_64 x86_64 GNU/Linux
> 
> For both d.vect and d.zoom SIGSEGV can be traced to G_whoami () at whoami.c:64.
Here is GDB stack trace:

> #2  0x0000002a95deb05b in db_version (driver=0x50c4b8,
>     client_version=0x50c4bc, driver_version=0x50c4c0) at c_version.c:20
> #3  0x0000002a97be6a01 in __db_e_attach () from /usr/lib64/tls/libdb-4.2.so
libdb is calling db_version, expecting to call its own function of
that name, but it's actually calling the one in libgrass_dbmiclient.

I'm not sure that there's any solution other than to rename the DBMI
functions to use a different prefix (one which isn't already used by a
common system library).

-- 
Glynn Clements <glynn@gclements.plus.com>


Thu, Apr 27 2006 23:17:44    Mail sent by sorokina@ornl.gov  
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Date Thu, 27 Apr 2006 17:17:34 -0400
From "Sorokine, Alexandre" <sorokina@ornl.gov>
Subject RE: [bug #4349] (grass) Segfault in several display modules on x86_64
To Glynn Clements via RT <grass-bugs@intevation.de>
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Glynn,

Thank you very much for your help!

db_version from grass DBMI interface conflicts with db_version from
Berkley DB libdb.so.  There are only five function in Berkeley DB that
use db_ prefix.  These functions are db_create, db_env_create,
db_strerr, db_seq_create and db_version.  I think that it would be
enough to rename db_version in GRASS DBMI interface as there are no
other collisions with Berkeley DB.  Berkeley DB library is loaded if
ldap is used for the name resolution.

"find . -name \*.h -o -name \*.c | xargs grep db_version" shows only two
file in GRASS source tree that use db_version, the following patch
solves the problem on my system (I renamed db_version into
db_dbmi_version):

Index: ./lib/db/dbmi_client/c_version.c
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
RCS file:
/home/grass/grassrepository/grass6/lib/db/dbmi_client/c_version.c,v
retrieving revision 1.3
diff -u -r1.3 c_version.c
--- ./lib/db/dbmi_client/c_version.c    9 Feb 2006 03:08:54 -0000
1.3
+++ ./lib/db/dbmi_client/c_version.c    27 Apr 2006 21:16:20 -0000
@@ -7,7 +7,7 @@
  \return
  \param
 */
-db_version (dbDriver *driver, dbString *client_version, dbString
*driver_version)
+db_dbmi_version (dbDriver *driver, dbString *client_version, dbString
*driver_version)

 {
     int ret_code;
Index: ./include/proto_dbmi.h
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
RCS file: /home/grass/grassrepository/grass6/include/proto_dbmi.h,v
retrieving revision 1.24
diff -u -r1.24 proto_dbmi.h
--- ./include/proto_dbmi.h      16 Dec 2005 10:01:33 -0000      1.24
+++ ./include/proto_dbmi.h      27 Apr 2006 21:16:21 -0000
@@ -363,7 +363,7 @@
 void        db_unset_cursor_mode_insensitive P((dbCursor *cursor ));
 void        db_unset_cursor_mode_scroll P((dbCursor *cursor ));
 int         db_update                 P((dbCursor *cursor ));
-int         db_version                P((dbDriver *driver , dbString
*client_version , dbString *driver_version ));
+int         db_dbmi_version                P((dbDriver *driver ,
dbString *client_version , dbString *driver_version ));
 char *      db_whoami                 P((void ));
 void        db_zero                   P((void *s , int n ));
 void         db_zero_string            P((dbString *x ));

--
Alex Sorokine, Ph.D. <sorokina@ornl.gov>
Oak Ridge National Lab
=20

> -----Original Message-----
> From: Glynn Clements via RT [mailto:grass-bugs@intevation.de]=20
> Sent: Thursday, April 27, 2006 12:24 PM
> To: Sorokine, Alexandre
> Subject: [bug #4349] (grass) Segfault in several display=20
> modules on x86_64
>=20
>=20
> Request Tracker wrote:
>=20
> > this bug's URL: http://intevation.de/rt/webrt?serial_num=3D4349
> >=20
> --------------------------------------------------------------
> -----------
> >=20
> > Subject: Segfault in several display modules on x86_64=20
> >=20
> > Platform: GNU/Linux/x86_64
> > grass binary for platform: Compiled from Sources
> > GRASS Version: GRASS 6.1.cvs (2006) checkout 4/22/06
> >=20
> > Segfault in several display modules (d.vect, d.zoom) on=20
> x86_64, Suse 9.2. =20
> >=20
> > uname -a:
> >=20
> > Linux node0 2.6.5-7.244_lustre.1.4.6smp #1 SMP Sat Feb 18=20
> 17:33:39 EST 2006 x86_64 x86_64 x86_64 GNU/Linux
> >=20
> > For both d.vect and d.zoom SIGSEGV can be traced to=20
> G_whoami () at whoami.c:64.  Here is GDB stack trace:
>=20
> > #2  0x0000002a95deb05b in db_version (driver=3D0x50c4b8,
> >     client_version=3D0x50c4bc, driver_version=3D0x50c4c0) at=20
> c_version.c:20
> > #3  0x0000002a97be6a01 in __db_e_attach () from=20
> /usr/lib64/tls/libdb-4.2.so
>=20
> libdb is calling db_version, expecting to call its own function of
> that name, but it's actually calling the one in libgrass_dbmiclient.
>=20
> I'm not sure that there's any solution other than to rename the DBMI
> functions to use a different prefix (one which isn't already used by a
> common system library).
>=20
> --=20
> Glynn Clements <glynn@gclements.plus.com>
>=20
>=20
> --- Headers Follow ---
>=20
> >From glynn@gclements.plus.com  Thu Apr 27 18:24:25 2006
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> Received: from cerise.gclements.plus.com=20
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> 	Thu, 27 Apr 2006 17:24:19 +0100
> From: Glynn Clements <glynn@gclements.plus.com>
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> Date: Thu, 27 Apr 2006 17:24:19 +0100
> To: Request Tracker <grass-bugs@intevation.de>
> Cc: grass5@grass.itc.it
> Subject: Re: [GRASS5] [bug #4349] (grass) Segfault in several=20
> display modules on x86_64
> In-Reply-To: <20060426204143.E1BC41005CD@lists.intevation.de>
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> Request Tracker
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Thu, Apr 27 2006 23:25:44    Mail sent by neteler@itc.it  
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Date Thu, 27 Apr 2006 23:25:37 +0200
From Markus Neteler <neteler@itc.it>
To Glynn Clements <glynn@gclements.plus.com>
Cc Request Tracker <grass-bugs@intevation.de>, grass5@grass.itc.it
Subject Re: [GRASS5] [bug #4349] (grass) Segfault in several display modules on x86_64
Message-ID <20060427212537.GB20868@bartok.itc.it>
Mail-Followup-To Glynn Clements <glynn@gclements.plus.com>, Request Tracker <grass-bugs@intevation.de>, grass5@grass.itc.it
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On Thu, Apr 27, 2006 at 05:24:19PM +0100, Glynn Clements wrote:
> 
> Request Tracker wrote:
> 
> > this bug's URL: http://intevation.de/rt/webrt?serial_num=4349
> > -------------------------------------------------------------------------
> > 
> > Subject: Segfault in several display modules on x86_64 
> > 
> > Platform: GNU/Linux/x86_64
> > grass binary for platform: Compiled from Sources
> > GRASS Version: GRASS 6.1.cvs (2006) checkout 4/22/06
> > 
> > Segfault in several display modules (d.vect, d.zoom) on x86_64, Suse 9.2.
> > 
> > uname -a:
> > 
> > Linux node0 2.6.5-7.244_lustre.1.4.6smp #1 SMP Sat Feb 18 17:33:39 EST 2006
x86_64 x86_64 x86_64 GNU/Linux
> > 
> > For both d.vect and d.zoom SIGSEGV can be traced to G_whoami () at whoami.c:64.
Here is GDB stack trace:
> 
> > #2  0x0000002a95deb05b in db_version (driver=0x50c4b8,
> >     client_version=0x50c4bc, driver_version=0x50c4c0) at c_version.c:20
> > #3  0x0000002a97be6a01 in __db_e_attach () from /usr/lib64/tls/libdb-4.2.so
> 
> libdb is calling db_version, expecting to call its own function of
> that name, but it's actually calling the one in libgrass_dbmiclient.
> 
> I'm not sure that there's any solution other than to rename the DBMI
> functions to use a different prefix (one which isn't already used by a
> common system library).

Maybe

 db_gversion

? Wow, NO hit in google.

Markus


Fri, Apr 28 2006 03:46:15    Mail sent by hamish_nospam@yahoo.com  
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Date Fri, 28 Apr 2006 13:44:54 +1200
From Hamish <hamish_nospam@yahoo.com>
To Markus Neteler <neteler@itc.it>
Cc glynn@gclements.plus.com, grass-bugs@intevation.de, grass5@grass.itc.it
Subject Re: [GRASS5] [bug #4349] (grass) Segfault in several display modules on x86_64
Message-Id <20060428134454.7103344d.hamish_nospam@yahoo.com>
In-Reply-To <20060427212537.GB20868@bartok.itc.it>
References <20060426204143.E1BC41005CD@lists.intevation.de> <17488.61491.514272.913672@cerise.gclements.plus.com> <20060427212537.GB20868@bartok.itc.it>
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> > libdb is calling db_version, expecting to call its own function of
> > that name, but it's actually calling the one in libgrass_dbmiclient.
> > 
> > I'm not sure that there's any solution other than to rename the DBMI
> > functions to use a different prefix (one which isn't already used by
> > a common system library).
> 
> Maybe
> 
>  db_gversion

That's for that one function, there are lots of generic-named fns in the
dmbi lib like db_delete() etc.. 

maybe make them all dbmi_* ?  I guess gdb_ is no good.. :)

DB_* 
?

Hamish


Fri, Apr 28 2006 19:08:54    Mail sent by glynn@gclements.plus.com  
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Date Fri, 28 Apr 2006 18:08:48 +0100
To Hamish <hamish_nospam@yahoo.com>
Cc Markus Neteler <neteler@itc.it>, grass-bugs@intevation.de, grass5@grass.itc.it
Subject Re: [GRASS5] [bug #4349] (grass) Segfault in several display modules on x86_64
In-Reply-To <20060428134454.7103344d.hamish_nospam@yahoo.com>
References <20060426204143.E1BC41005CD@lists.intevation.de> <17488.61491.514272.913672@cerise.gclements.plus.com> <20060427212537.GB20868@bartok.itc.it> <20060428134454.7103344d.hamish_nospam@yahoo.com>
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Hamish wrote:

> > > libdb is calling db_version, expecting to call its own function of
> > > that name, but it's actually calling the one in libgrass_dbmiclient.
> > > 
> > > I'm not sure that there's any solution other than to rename the DBMI
> > > functions to use a different prefix (one which isn't already used by
> > > a common system library).
> > 
> > Maybe
> > 
> >  db_gversion
> 
> That's for that one function, there are lots of generic-named fns in the
> dmbi lib like db_delete() etc.. 
> 
> maybe make them all dbmi_* ?  I guess gdb_ is no good.. :)
> 
> DB_* 
> ?

That's what I thought. Then I remembered that the linker might not be
case sensitive. Then, I realised that if the linker isn't case
sensitive, using GRASS in a GTK+ is out of the question, as libgis
(G_*) will conflict with glib (g_*), e.g. G_malloc() vs g_malloc().

DBMI_* would probably be safe enough.

In any case, renaming all of the db_* functions isn't really an option
Doing it by hand is out of the question (275 source files). A script
to change identifiers beginning with db_ might change variable or type
names.

Fortunately, the Berkely DB library only exports a few functions
beginning with "db_" (the main interface is via function pointers in
the DB structure). Apart from the 19 db_env_set_func_* functions, it
only exports:

	db_create
	db_env_create
	db_strerror
	db_version

db_version is the only one which currently conflicts with the DBMI
library.

-- 
Glynn Clements <glynn@gclements.plus.com>


Sun, Apr 30 2006 21:34:45    Mail sent by mneteler  
Hi,

I have updated
 include/proto_dbmi.h
 lib/db/dbmi_client/c_version.c

and renamed it (for now) to
db_gversion().

Please test and report.

thanks

 Markus
Mon, May 1 2006 20:46:58    Mail sent by sorokina@ornl.gov  
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Date Mon, 01 May 2006 14:46:51 -0400
From "Sorokine, Alexandre" <sorokina@ornl.gov>
Subject RE: [bug #4349] (grass) Segfault in several display modules on x86_64
To Markus Neteler via RT <grass-bugs@intevation.de>
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Thread-Topic [bug #4349] (grass) Segfault in several display modules on x86_64
Thread-Index AcZsjSiQOS5Qp7v9R6CLSMoKrFmZRAAwk9+g
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Markus,

I've tested the patch, works fine for me.  Platforms tested:

RHEL4 x86
SUSE 9.1 x86_64


--
Alex Sorokine, Ph.D. <sorokina@ornl.gov>
Oak Ridge National Lab
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> -----Original Message-----
> From: Markus Neteler via RT [mailto:grass-bugs@intevation.de]=20
> Sent: Sunday, April 30, 2006 3:35 PM
> To: Sorokine, Alexandre
> Subject: [bug #4349] (grass) Segfault in several display=20
> modules on x86_64
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> Hi,
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> I have updated
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>  include/proto_dbmi.h
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>  lib/db/dbmi_client/c_version.c
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> and renamed it (for now) to
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> db_gversion().
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> Please test and report.
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> thanks
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>  Markus
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> -------------------------------------------- Managed by=20
> Request Tracker
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Wed, May 3 2006 08:28:01    Status changed to resolved by hbowman  
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