Re: [AMBER] ptraj error with *** glibc detected *** ptraj: free(): invalid next size (normal)

From: Bongkeun Kim <bkim.chem.ucsb.edu>
Date: Tue, 07 Jun 2011 14:29:46 -0700

Hello,

I found that this error occurred at the computer that was installed
with AmberTools 1.5 with bugfix 4. We installed it only on one
computer and that gives this error.
I attached the first 10 snapshots from the big traj file and pdb file
for reference pdb for rms calculation.
The input script you can use is following;
----------------------
#!/bin/bash
   ptraj beta.prmtop <<EOF
trajin remd3.Ttraj.273.8.crd
reference beta2.pdb
rms reference out rmsr3.273.8.dat :1-16.N,CA,C
radgyr out rg3.273.8.dat :1-16
distance d1 :1.CA :16.CA out dist3.273.8.dat
rms first out rms3.273.8.dat :1-16
go
EOF
--------------------------------
Thank you.
Bongkeun Kim




Quoting Daniel Roe <daniel.r.roe.gmail.com>:

> 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 - 15:00:05 PDT
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