AMBER Archive (2006)

Subject: AMBER: General Coding Problem

From: Elijah Gregory (
Date: Mon Oct 16 2006 - 18:53:27 CDT

Dear AMBER developers,

   I'm sorry for the indirect AMBER question, but figure it is
something to be answered or dismissed very quickly. I am coding a
routine for ptraj and it seems to run fine until the end of execution.

  The backtrace is:

Program received signal SIGABRT, Aborted.
0xffffe405 in __kernel_vsyscall ()
(gdb) bt
#0 0xffffe405 in __kernel_vsyscall ()
#1 0x555e37a5 in raise () from /lib/tls/
#2 0x555e5209 in abort () from /lib/tls/
#3 0x5561771a in __libc_message () from /lib/tls/
#4 0x5561dfbf in _int_free () from /lib/tls/
#5 0x5561e33a in free () from /lib/tls/
#6 0x0805fee5 in safe_free (pointer=0x80cb790) at utility.c:222
#7 0x08073dd7 in ptrajClearState (stateinp=0xffffcab0) at ptraj.c:1860
#8 0x0807b55b in ptraj (filenamep=0x0) at ptraj.c:5163
#9 0x0806a139 in interface (mode=INTERFACE_PTRAJ, filename=0x0) at
#10 0x0804935f in main (argCount=1, argPointer=0xffffd494) at main.c:173

I am just curious whether anyone knows what role __kernel_vsyscall()
plays? It is a subroutine in and hopefully by knowing it's
role I can decipher what the error is trying to tell me.


Elijah Gregory
UCSD, Dept. Chem. and Biochem.
Ph.D. Student
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