Hi Dan,
Thanks for your reply.
I would install the upgraded ptraj from AmberTools 12.
I was using the ptraj and part of the input file is described below:
trajin /home/usr/prod_1ns.mdcrd.gz
trajin /home/usr/prod_2ns.mdcrd.gz
trajin /home/usr/prod_3ns.mdcrd.gz
trajin /home/usr/prod_4ns.mdcrd.gz
trajin /home/usr/prod_5ns.mdcrd.gz
strip :WAT
strip :Cl-
center :1-200
image center familiar
rms first out rmsd-5ns :1-200.CA
atomicfluct out rmsf-5ns byres
However, in the mean time I am providing the entire error message came
while running ptraj as follows:
*** glibc detected *** /usr/apps/amber11/exe/ptraj: munmap_chunk(): invalid
pointer: 0x000000001faebfd0 ***
======= Backtrace: =========
/lib64/libc.so.6(cfree+0x1b6)[0x3008672b96]
/usr/apps/amber11/exe/ptraj[0x42194e]
/usr/apps/amber11/exe/ptraj[0x422a54]
/usr/apps/amber11/exe/ptraj[0x422b16]
/usr/apps/amber11/exe/ptraj[0x42a896]
/usr/apps/amber11/exe/ptraj[0x44a342]
/usr/apps/amber11/exe/ptraj[0x450c84]
/usr/apps/amber11/exe/ptraj[0x451c40]
/usr/apps/amber11/exe/ptraj[0x437d27]
/usr/apps/amber11/exe/ptraj[0x40272a]
/lib64/libc.so.6(__libc_start_main+0xf4)[0x300861d8a4]
/usr/apps/amber11/exe/ptraj[0x402339]
======= Memory map: ========
00400000-00557000 r-xp 00000000 fd:04 64836488
/usr/apps/amber11/bin/ptraj
00757000-00761000 rw-p 00157000 fd:04 64836488
/usr/apps/amber11/bin/ptraj
00761000-00765000 rw-p 00761000 00:00 0
1f6aa000-1fb13000 rw-p 1f6aa000 00:00 0
3008200000-300821a000 r-xp 00000000 fd:02 1106043
/lib64/ld-2.5.so
3008419000-300841a000 r--p 00019000 fd:02 1106043
/lib64/ld-2.5.so
300841a000-300841b000 rw-p 0001a000 fd:02 1106043
/lib64/ld-2.5.so
3008600000-3008746000 r-xp 00000000 fd:02 1106044
/lib64/libc-2.5.so
3008746000-3008946000 ---p 00146000 fd:02 1106044
/lib64/libc-2.5.so
3008946000-300894a000 r--p 00146000 fd:02 1106044
/lib64/libc-2.5.so
300894a000-300894b000 rw-p 0014a000 fd:02 1106044
/lib64/libc-2.5.so
300894b000-3008950000 rw-p 300894b000 00:00 0
3008e00000-3008e82000 r-xp 00000000 fd:02 1106052
/lib64/libm-2.5.so
3008e82000-3009081000 ---p 00082000 fd:02 1106052
/lib64/libm-2.5.so
3009081000-3009082000 r--p 00081000 fd:02 1106052
/lib64/libm-2.5.so
3009082000-3009083000 rw-p 00082000 fd:02 1106052
/lib64/libm-2.5.so
301a400000-301a40d000 r-xp 00000000 fd:02 1106058
/lib64/libgcc_s-4.1.2-20070626.so.1
301a40d000-301a60d000 ---p 0000d000 fd:02 1106058
/lib64/libgcc_s-4.1.2-20070626.so.1
301a60d000-301a60e000 rw-p 0000d000 fd:02 1106058
/lib64/libgcc_s-4.1.2-20070626.so.1
2aaaaaaab000-2aaaaaaae000 rw-p 2aaaaaaab000 00:00 0
2aaaaaab9000-2aaaaaaba000 rw-p 2aaaaaab9000 00:00 0
2aaaaaaba000-2aaaaab50000 r-xp 00000000 fd:02 481804
/usr/lib64/libgfortran.so.1.0.0
2aaaaab50000-2aaaaad4f000 ---p 00096000 fd:02 481804
/usr/lib64/libgfortran.so.1.0.0
2aaaaad4f000-2aaaaad51000 rw-p 00095000 fd:02 481804
/usr/lib64/libgfortran.so.1.0.0
2aaaaad51000-2aaaab3bd000 rw-p 2aaaaad51000 00:00 0
2aaaab3be000-2aaaac01b000 rw-p 2aaaab3be000 00:00 0
7fffea907000-7fffea91d000 rw-p 7fffea907000 00:00 0
[stack]
ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0
[vdso]
I hope, this error message may provide the clue to trace the fault.
best
Jagur
On Tue, Jan 22, 2013 at 7:53 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Without more information on what exactly you were trying to do it's
> difficult to determine why the memory error occurred. I would
> recommend upgrading to ptraj (or even cpptraj) from AmberTools 12
> (http://ambermd.org/AmberTools-get.html) which is far more stable.
>
> -Dan
>
> On Tue, Jan 22, 2013 at 4:55 PM, Jagur Lambix <jagurlambix.gmail.com>
> wrote:
> > Dear AMBER users,
> >
> > I was trying to run the ptraj and got to this information as follows:
> >
> > *** glibc detected *** /usr/amber11/exe/ptraj: munmap_chunk(): invalid
> > pointer: 0x000000000649bfc0 ***
> >
> > I tried to get the information from AMBER archive, but didn't find an
> exact
> > error similar to it.
> >
> > Can any one help me out here?
> >
> > Thanks in advanced for your help.
> >
> > Jagur
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-9119 (Fax)
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Jan 23 2013 - 08:00:02 PST
