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
>>>> >> >
>>>> >> >
>>>> >>
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>>>> >>
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>>>> >
>>>>
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>
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Received on Thu Sep 15 2011 - 06:00:02 PDT
