Hi,
Since you see this error on one computer only it's possible the
problem is with that computer. However, just to be certain could you
send me your ptraj input as well as a topology and restart file for
your system so I can attempt to reproduce the error? Thanks.
-Dan
On Mon, Jun 6, 2011 at 4:30 PM, Bongkeun Kim <bkim.chem.ucsb.edu> wrote:
> Dear AMBER,
>
> I got this error the end of ptraj run.
> After this error, mostly I got all the outputs without any problem.
> But ptraj just stopped in the middle of analysis run.
> I have several PCs, they are running Ubuntu 10.04 with nfs file
> system, so they have the same softare/hardware setup. But I can see
> this error from the only one computer always. Do you think this is
> because of hardware failure?
> I'm running AMBER 11 and AmberTools 1.4 and applied all the patches
> until April.
> The error messages are:
> ==================================================
> PTRAJ RMS: dumping RMSd vs time data
> *** glibc detected *** ptraj: free(): invalid next size (normal):
> 0x0000000001ecdd70 ***
> ======= Backtrace: =========
> /lib/libc.so.6(+0x775b6)[0x7f23882515b6]
> /lib/libc.so.6(cfree+0x73)[0x7f2388257e83]
> ptraj[0x4234f2]
> ptraj[0x44c5a9]
> ptraj[0x455753]
> ptraj[0x439c15]
> ptraj[0x402c41]
> /lib/libc.so.6(__libc_start_main+0xfd)[0x7f23881f8c4d]
> ptraj[0x4027b9]
> ======= Memory map: ========
> 00400000-0055f000 r-xp 00000000 00:15 301212899
> /home/bkim/packages/amber11/bin/ptraj
> 0075e000-0075f000 r--p 0015e000 00:15 301212899
> /home/bkim/packages/amber11/bin/ptraj
> 0075f000-00769000 rw-p 0015f000 00:15 301212899
> /home/bkim/packages/amber11/bin/ptraj
> 00769000-0076d000 rw-p 00000000 00:00 0
> 01eaa000-01f0d000 rw-p 00000000 00:00 0
> [heap]
> 7f2383de9000-7f2383dff000 r-xp 00000000 09:01 8110
> /lib/libgcc_s.so.1
> 7f2383dff000-7f2383ffe000 ---p 00016000 09:01 8110
> /lib/libgcc_s.so.1
> 7f2383ffe000-7f2383fff000 r--p 00015000 09:01 8110
> /lib/libgcc_s.so.1
> 7f2383fff000-7f2384000000 rw-p 00016000 09:01 8110
> /lib/libgcc_s.so.1
> 7f2384000000-7f2384021000 rw-p 00000000 00:00 0
> 7f2384021000-7f2388000000 ---p 00000000 00:00 0
> 7f23881da000-7f2388354000 r-xp 00000000 09:01 8429
> /lib/libc-2.11.1.so
> 7f2388354000-7f2388553000 ---p 0017a000 09:01 8429
> /lib/libc-2.11.1.so
> 7f2388553000-7f2388557000 r--p 00179000 09:01 8429
> /lib/libc-2.11.1.so
> 7f2388557000-7f2388558000 rw-p 0017d000 09:01 8429
> /lib/libc-2.11.1.so
> 7f2388558000-7f238855d000 rw-p 00000000 00:00 0
> 7f238855d000-7f23885df000 r-xp 00000000 09:01 8476
> /lib/libm-2.11.1.so
> 7f23885df000-7f23887de000 ---p 00082000 09:01 8476
> /lib/libm-2.11.1.so
> 7f23887de000-7f23887df000 r--p 00081000 09:01 8476
> /lib/libm-2.11.1.so
> 7f23887df000-7f23887e0000 rw-p 00082000 09:01 8476
> /lib/libm-2.11.1.so
> 7f23887e0000-7f23888cb000 r-xp 00000000 09:01 8108
> /usr/lib/libgfortran.so.3.0.0
> 7f23888cb000-7f2388aca000 ---p 000eb000 09:01 8108
> /usr/lib/libgfortran.so.3.0.0
> 7f2388aca000-7f2388acb000 r--p 000ea000 09:01 8108
> /usr/lib/libgfortran.so.3.0.0
> 7f2388acb000-7f2388acc000 rw-p 000eb000 09:01 8108
> /usr/lib/libgfortran.so.3.0.0
> 7f2388acc000-7f2388acd000 rw-p 00000000 00:00 0
> 7f2388acd000-7f2388aed000 r-xp 00000000 09:01 6737
> /lib/ld-2.11.1.so
> 7f2388bc5000-7f2388cc9000 rw-p 00000000 00:00 0
> 7f2388ce8000-7f2388cec000 rw-p 00000000 00:00 0
> 7f2388cec000-7f2388ced000 r--p 0001f000 09:01 6737
> /lib/ld-2.11.1.so
> 7f2388ced000-7f2388cee000 rw-p 00020000 09:01 6737
> /lib/ld-2.11.1.so
> 7f2388cee000-7f2388cef000 rw-p 00000000 00:00 0
> 7fff18bed000-7fff18c02000 rw-p 00000000 00:00 0
> [stack]
> 7fff18d46000-7fff18d47000 r-xp 00000000 00:00 0
> [vdso]
> ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0
> [vsyscall]
> ./analyze_all_temps.x: line 5: 1184 Aborted ptraj
> beta.prmtop <<EOF
> ==============================================
> Thank you.
> Bongkeun Kim
>
>
>
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Received on Tue Jun 07 2011 - 04:30:05 PDT
