[xcrysden] problem in compiling Xcrysden

Tue Mar 13 13:18:06 CET 2012

dear prof. Kokalj,yes our system has gdb installed. i recompiled the package and it crashed again.this time command "WHERE" resulted in : "Program received signal SIGSEGV, Segmentation fault.
0x00000030c7873155 in _int_malloc () from /lib64/libc.so.6
(gdb) Quit
(gdb) where
#0  0x00000030c7873155 in _int_malloc () from /lib64/libc.so.6
#1  0x00000030c7874e2e in malloc () from /lib64/libc.so.6
#2  0x00000030c78754e8 in realloc () from /lib64/libc.so.6
#3  0x0000000000462b7a in xcRealloc (ptr=0x0, size=1336) at memory.c:47
#4  0x0000000000481480 in cryIsosurfClip (in=0x1184820, n=..., p0=...) at cryClip.c:236
#5  0x000000000047a969 in CropBz_New (wc=0x108b2c0, iso=0x108acb0) at fs.c:257
#6  0x0000000000480a33 in CRY_SurfCmd (clientData=0x778010, interp=0x737340, argc=26, argv=0x739aa0) at crySurf.c:540
#7  0x00002aaaab123fbf in TclInvokeStringCommand () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#8  0x00002aaaab1251b9 in TclEvalObjvInternal () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#9  0x00002aaaab167d70 in TclExecuteByteCode () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#10 0x00002aaaab1a79ad in TclObjInterpProcCore () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#11 0x00002aaaab1251b9 in TclEvalObjvInternal () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#12 0x00002aaaab167d70 in TclExecuteByteCode () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#13 0x00002aaaab1a79ad in TclObjInterpProcCore () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#14 0x00002aaaab1251b9 in TclEvalObjvInternal () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#15 0x00002aaaab126393 in Tcl_EvalObjv () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#16 0x00002aaaab1267f0 in TclEvalObjEx () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#17 0x00002aaaab1a8321 in Tcl_UplevelObjCmd () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#18 0x00002aaaab1251b9 in TclEvalObjvInternal () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#19 0x00002aaaab167d70 in TclExecuteByteCode () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#20 0x00002aaaab1a79ad in TclObjInterpProcCore () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#21 0x00002aaaab1251b9 in TclEvalObjvInternal () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#22 0x00002aaaab125e16 in TclEvalEx () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#23 0x00002aaaab126196 in Tcl_EvalEx () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#24 0x00002aaaaadf1da2 in Tk_BindEvent () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so
#25 0x00002aaaaae3394d in CanvasDoEvent () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so
#26 0x00002aaaaae345af in CanvasBindProc () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so
#27 0x00002aaaaadfca24 in Tk_HandleEvent () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so
#28 0x00002aaaaadfcce0 in WindowEventProc () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so
#29 0x00002aaaab19951d in Tcl_ServiceEvent () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#30 0x00002aaaab19978e in Tcl_DoOneEvent () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so
#31 0x00002aaaaadfc24b in Tk_MainLoop () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so
#32 0x00002aaaaae09827 in Tk_MainEx () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so
#33 0x0000000000405a60 in main (argc=4, argv=0x7fffffffd368) at xcAppInit.c:412
"i don't know if this info points any where or not !Regards,M. Arshad Farhan
 > From: tone.kokalj at ijs.si
> To: xcrysden at democritos.it
> Date: Tue, 13 Mar 2012 09:45:44 +0100
> Subject: Re: [xcrysden] problem in compiling Xcrysden
> 
> On Tue, 2012-03-13 at 17:27 +0900, محمد ارشد فرحان wrote:
> > Dear Prof. Kokalj,
> > thank you very much for your help.
> > i had successfully compiled Xcrysden-1.5.53 ; however when i executed
> > the program for FERMI SURFACE rendering, it crashed just like the
> > previous version (the reason why i started to compile it again).
> > the error reads:
> > "*** glibc detected
> > *** /home/mafarhan/programs/xcrysden-1.5.53/bin/xcrys: free(): invalid
> > next size (normal): 0x000000001bf55700 ***
> 
> Check if you have gdb debugger and if so, then compile xcrysden
> with enabled debugging (i.e. set CFLAGS = -g in Make.sys). Do:
> 
> 1. make clean
> 2. make xcrysden
> 3. ./xcrysden -d
> 
> and after crash say "where" in the gdb prompt. Perhaps the message will
> be informative. Send me the info.
> 
> Regards, Tone
> 
> -- 
> Anton Kokalj
> J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 
> (tel: +386-1-477-3523 // fax:+386-1-477-3822)
> 
> Please, if possible, avoid sending me Word or PowerPoint attachments.
> See:  http://www.gnu.org/philosophy/no-word-attachments.html
> 
> _______________________________________________
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> XCrySDen at democritos.it
> http://www.democritos.it/mailman/listinfo/xcrysden
 		 	   		  
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