Dear Dan,
Please find attached the entire output.
Thanks,
Praapti
On Thu, Sep 15, 2011 at 6:12 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Your attached log only contains the line
>
> "Segmentation fault"
>
> I need the entire output (stdout and stderr), like what I had attached
> in my previous email. So it should look like:
>
> CPPTRAJ: Trajectory Analysis. V1.1.1
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> > [noprogress]
> ...
>
> For example, if your top file is "prmtop" and your input file is
> "cpptraj.in" you can write all output to one file (cpptraj.log) by
> running:
>
> cpptraj prmtop cpptraj.in > cpptraj.log 2>&1
>
> -Dan
>
> On Tue, Sep 13, 2011 at 12:37 AM, Praapti Jayaswal <praapti.gmail.com>
> wrote:
> > Dear Dan,
> >
> > Please find attached the complete output of cpptraj from a run that
> > segfaults (wt-log) and the details of compilers and their versions.
> > While configuring Amber , I used the guidelines given in
> > the manual.
> >
> > Thanks,
> >
> > Praapti
> >
> > On 9/12/11, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> >> Hi,
> >>
> >> I cannot reproduce your error using a 10 frame trajectory file created
> >> from the PDB you sent, and valgrind shows no memory errors or leaks
> >> (see attached output). In order to debug this further I'm going to
> >> need more information. Can you 1) send me the complete output (stdout
> >> + stderr) of cpptraj from a run that segfaults, 2) let me know what
> >> compilers you are using and what version, and 3) let me know what
> >> flags you specified when configuring Amber. Thanks!
> >>
> >> -Dan
> >>
> >> On Mon, Sep 12, 2011 at 2:58 AM, Praapti Jayaswal <praapti.gmail.com>
> wrote:
> >>> Dear Dan,
> >>>
> >>> I applied the new patch (bugfix.16) and reinstalled Amber11. However,
> >>> segmentation fault persists when i try to calculate rmsd using cpptraj
> for
> >>> more than one frame of trajectory, when waters are stripped. I have
> also
> >>> tried the above mentioned exercise on other Linux Systems, but the
> >>> segmentation fault persists.
> >>>
> >>> Please suggest a solution!
> >>>
> >>> Praapti
> >>>
> >>> On Tue, Sep 6, 2011 at 5:56 AM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >>>
> >>>> Hi,
> >>>>
> >>>> There is now a patch posted (bugfix.16) that should fix this. Let me
> >>>> know if the problem is still occurring after applying the patch (make
> >>>> sure that bugfixes 1-15 have already been applied).
> >>>>
> >>>> http://ambermd.org/bugfixesat.html
> >>>>
> >>>> -Dan
> >>>>
> >>>> On Mon, Sep 5, 2011 at 12:01 AM, Praapti Jayaswal <praapti.gmail.com>
> >>>> wrote:
> >>>> > The command works perfectly if :
> >>>> > (i) I use the entire solvated trajectory for calculating rmsd for
> more
> >>>> than
> >>>> > one frame, or
> >>>> > (ii) if I calculate rmsd for one frame when waters are stripped.
> >>>> >
> >>>> > However, segmentation fault occurs when I try to calculate rmsd
> using
> >>>> > cpptraj for more than one frame when waters are stripped.
> >>>> >
> >>>> > Praapti
> >>>> >
> >>>> >
> >>>> >
> >>>> > On Sat, Sep 3, 2011 at 4:00 AM, Daniel Roe <daniel.r.roe.gmail.com>
> >>>> wrote:
> >>>> >
> >>>> >> Hi,
> >>>> >>
> >>>> >> I couldn't reproduce this error - however, I notice that your
> 'range'
> >>>> >> argument is 1-160, while you only have 154 residues in your
> topology.
> >>>> >> I looked at the code and it's possible that this could cause a
> >>>> >> segfault on some systems. Try this command instead and let me know
> if
> >>>> >> the segfault goes away:
> >>>> >>
> >>>> >> rmsd :1-154 reference perres range 1-154 perresout back.tmp
> perresmask
> >>>> >> .CA,C,O,N
> >>>> >>
> >>>> >> In the meantime I will work on a patch.
> >>>> >>
> >>>> >> -Dan
> >>>> >>
> >>>> >> On Thu, Sep 1, 2011 at 2:02 AM, Praapti Jayaswal <
> praapti.gmail.com>
> >>>> >> wrote:
> >>>> >> > Hi All,
> >>>> >> >
> >>>> >> > With reference to the query posted by my colleague, Xiao Chen (
> >>>> >> > http://archive.ambermd.org/201106/0259.html), I am also getting
> >>>> >> segmentation
> >>>> >> > fault , when i run cpptraj to calculate rmsd for the residues
> using
> >>>> >> > trajectory (with waters stripped, i.e. wt_dry.mdcrd).
> >>>> >> >
> >>>> >> >
> >>>> >> > trajin wt_dry.mdcrd
> >>>> >> > reference wt.pdb
> >>>> >> > rmsd :1-160 reference perres range 1-160 perresout back.tmp
> >>>> >> > perresmask
> >>>> >> > .CA,C,O,N
> >>>> >> > go
> >>>> >> >
> >>>> >> > cpptraj wt_dry.prmtop cpptraj_rmsd.in
> >>>> >> >
> >>>> >> >
> >>>> >> >
> >>>> >> > I have performed bugfix for ambertools 1.5 on
> >>>> >> > Linux.<http://archive.ambermd.org/201106/0242.html>
> >>>> >> >
> >>>> >> > Please find attached the pdb file, since the size of the
> parameter
> >>>> >> > and
> >>>> >> > trajectory files exceeds permissible size limit.
> >>>> >> >
> >>>> >> > Could you please help??
> >>>> >> >
> >>>> >> > Thanks,
> >>>> >> >
> >>>> >> > Praapti
> >>>> >> >
> >>>> >> > _______________________________________________
> >>>> >> > AMBER mailing list
> >>>> >> > AMBER.ambermd.org
> >>>> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >>>> >> >
> >>>> >> >
> >>>> >>
> >>>> >> _______________________________________________
> >>>> >> AMBER mailing list
> >>>> >> AMBER.ambermd.org
> >>>> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>>> >>
> >>>> > _______________________________________________
> >>>> > AMBER mailing list
> >>>> > AMBER.ambermd.org
> >>>> > http://lists.ambermd.org/mailman/listinfo/amber
> >>>> >
> >>>>
> >>>> _______________________________________________
> >>>> AMBER mailing list
> >>>> AMBER.ambermd.org
> >>>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>>
> >>> _______________________________________________
> >>> AMBER mailing list
> >>> AMBER.ambermd.org
> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 15 2011 - 21:30:03 PDT
