Hi David,
Could you please provide some more information on these segmentation
faults? What version of ptraj do you have, what bugfixes have you
applied, what architecture are you running on, how large and how long
are the trajectories, and what kind of input to ptraj produces the
segmentation fault? You certainly shouldn't be getting them as a
regular occurrence. I'd be happy to try and track down and fix any
errors.
-Dan
On Monday, February 21, 2011, david condon <dec986.gmail.com> wrote:
> I receive segmentation faults often when running ptraj. However, I
> never use "contacts". I use mainly distance and dihedral.
>
> On 2/21/11, Daniel Roe <daniel.r.roe.gmail.com> wrote:
>> Thanks for the info, good to know it seems isolated to the 'contacts'
>> command.
>>
>> I'm not all that familiar with 'contacts' but I think that it's
>> relatively memory-intensive compared to most other actions. I can't
>> reproduce your error with a 1000 frame trajectory of a ~50K atom
>> system. It seems your system is much larger - could you provide the
>> topology and a restart file so I can try to reproduce the error (also
>> let me know about how many frames your traj is)? Thanks.
>>
>> -Dan
>>
>> On Mon, Feb 21, 2011 at 4:18 PM, Seibold, Stephen <Seibold79.stmary.edu>
>> wrote:
>>> Hi Dan
>>> Yes. Rdparm reads through correctly, stating the number of sets in the
>>> trajectory. RMSD and distances can be also calculated without a problem.
>>>
>>> Thanks Steve
>>>
>>>
>>> -----Original Message-----
>>> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
>>> Sent: Monday, February 21, 2011 3:00 PM
>>> To: AMBER Mailing List
>>> Subject: Re: [AMBER] PTRAJ and segmentation faults
>>>
>>> Hi,
>>>
>>> Is ptraj able to read through the trajectory at all? Does the segfault
>>> occur without the 'contacts' command?
>>>
>>> -Dan
>>>
>>> On Mon, Feb 21, 2011 at 3:56 PM, Seibold, Stephen <Seibold79.stmary.edu>
>>> wrote:
>>>> Hi users
>>>> I am having problems with the latest ToolSet version. I tried running
>>>> "contacts" in ptraj and keep getting a "segmentation fault". I am sending
>>>> you my input file and log file.
>>>>
>>>> Am I doing something wrong? I also tried using a PDB as input instead of
>>>> .mdcrd, but it also gave me the segmentation fault.
>>>>
>>>> INPUT:
>>>>
>>>> trajin RNAP_openMD39_42.mdcrd
>>>>
>>>> center :1-2495 mass origin
>>>> image origin center familiar
>>>>
>>>> contacts first byresidue out contact.txt time 10 distance 5.0 .CD
>>>>
>>>>
>>>> go
>>>>
>>>>
>>>> OUTPUT LOG FILE:
>>>>
>>>> \-/
>>>> -/- PTRAJ: a utility for processing trajectory files
>>>> /-\
>>>> \-/ Version: "AMBER 11.0 integrated" (4/2010)
>>>> -/- Executable is: "ptraj"
>>>> /-\ Running on 1 processor(s)
>>>> \-/ Residue labels:
>>>>
>>>> MET GLU ILE LYS ARG PHE GLY ARG ILE ARG
>>>> GLU VAL ILE PRO LEU PRO PRO LEU THR GLU
>>>> ILE GLN VAL GLU SER TYR ARG ARG ALA LEU
>>>> GLN ALA ASP VAL PRO PRO GLU LYS ARG GLU
>>>> ASN VAL GLY ILE GLN ALA ALA PHE ARG GLU
>>>> THR PHE PRO ILE GLU GLU GLU ASP LYS GLY
>>>> LYS GLY GLY LEU VAL LEU ASP PHE LEU GLU
>>>> TYR ARG LEU GLY GLU PRO PRO PHE PRO GLN
>>>> ............
>>>> ............
>>>>
>>>> WAT WAT WAT WAT WAT WAT WAT
>>>>
>>>> PRMTOP does not contain %FLAG RADIUS_SET
>>>> Setting box to be an exact truncated octahedron, angle is 109.471221
>>>>
>>>> PTRAJ: Processing input from "STDIN" ...
>>>>
>>>> PTRAJ: trajin RNAP_openMD39_42.mdcrd
>>>> Checking coordinates: RNAP_openMD39_42.mdcrd
>>>> ./ptraj: line 1: 5109 Segmentation fault ptraj RNAP_open.prmtop
>>>>
>>>>
>>>>
>>>> I applied all the new patches, recompiled (gc
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Received on Mon Feb 21 2011 - 20:30:06 PST
