AMBER Archive (2005)

Subject: AMBER: ptraj crash error

From: Simon Whitehead (SJW084_at_bham.ac.uk)
Date: Fri Dec 02 2005 - 11:51:47 CST

Dear amber users,

Having finally managed to get amber to compile on fedora core 4 using ifort 9.0 i tried to run some trajectory data through ptraj it aborted. I was trying to carryout the following command;

rms first out rms1.out :@CA

This resulted in the follwing error;

*** glibc detected *** ptraj: free(): invalid pointer: 0x008f58c0 ***
======= Backtrace: =========
/lib/libc.so.6[0x831424]
/lib/libc.so.6(__libc_free+0x77)[0x83195f]
ptraj[0x806dcfc]
ptraj[0x806e22a]
ptraj[0x808e20f]
ptraj[0x807538f]
ptraj[0x805e9a4]
ptraj[0x8075abf]
ptraj[0x8067d8b]
ptraj[0x804a7a4]
/lib/libc.so.6(__libc_start_main+0xc6)[0x7e2de6]
ptraj[0x804a631]
======= Memory map: ========
00111000-002eb000 r-xp 00000000 fd:00 491075 /opt/intel/fc/9.0/lib/libimf.so
002eb000-002ed000 rwxp 001d9000 fd:00 491075 /opt/intel/fc/9.0/lib/libimf.so
002ed000-003d8000 rwxp 002ed000 00:00 0
003d8000-003d9000 r-xp 003d8000 00:00 0
003d9000-00782000 rwxp 003d9000 00:00 0
00790000-00799000 r-xp 00000000 fd:00 1722081 /lib/libgcc_s-4.0.0-20050520.so.1
00799000-0079a000 rwxp 00009000 fd:00 1722081 /lib/libgcc_s-4.0.0-20050520.so.1
007b0000-007ca000 r-xp 00000000 fd:00 1722075 /lib/ld-2.3.5.so
007ca000-007cb000 r-xp 00019000 fd:00 1722075 /lib/ld-2.3.5.so
007cb000-007cc000 rwxp 0001a000 fd:00 1722075 /lib/ld-2.3.5.so
007ce000-008f2000 r-xp 00000000 fd:00 1722076 /lib/libc-2.3.5.so
008f2000-008f4000 r-xp 00124000 fd:00 1722076 /lib/libc-2.3.5.so
008f4000-008f6000 rwxp 00126000 fd:00 1722076 /lib/libc-2.3.5.so
008f6000-008f8000 rwxp 008f6000 00:00 0
008fa000-0091c000 r-xp 00000000 fd:00 1722080 /lib/libm-2.3.5.so
0091c000-0091d000 r-xp 00021000 fd:00 1722080 /lib/libm-2.3.5.so
0091d000-0091e000 rwxp 00022000 fd:00 1722080 /lib/libm-2.3.5.so
0091e000-00a3c000 rwxp 0091e000 00:00 0
00a4a000-00ad2000 rwxp 00a4a000 00:00 0
00aef000-00bbe000 rwxp 00aef000 00:00 0
00bd2000-00cb6000 rwxp 00bd2000 00:00 0
00cc8000-01370000 rwxp 00cc8000 00:00 0
05a37000-05a7f000 rwxp 05a37000 00:00 0
0643d000-06485000 rwxp 0643d000 00:00 0
068e0000-06970000 rwxp 068e0000 00:00 0
08048000-08121000 r-xp 00000000 fd:00 717680 /software/amber8/exe/ptraj
08121000-0812a000 rwxp 000d8000 fd:00 717680 /software/amber8/exe/ptraj
0812a000-08130000 rwxp 0812a000 00:00 0
08641000-0869b000 rwxp 08641000 00:00 0
087b3000-088a8000 rwxp 087b3000 00:00 0 [heap]
b7e00000-b7e21000 rwxp b7e00000 00:00 0
b7e21000-b7f00000 --xp b7e21000 00:00 0
bf968000-bf97e000 rwxp bf968000 00:00 0 [stack]
Abort

Has anyone any ideas/suggestions?

Many thanks in advance

Simon Whitehead

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