Hi,
I have finally been able to reproduce this error by expanding the mask
used in 'contacts' to include more atoms (for some reason the number
causing segfault in this case is 183 residues). I will continue to
work on this and update you as soon as I locate the source of the
error.
-Dan
On Sun, Feb 27, 2011 at 1:53 PM, Seibold, Stephen <Seibold79.stmary.edu> wrote:
> Hi Dan
> I gathered trajectories using NetCDF (20 sets) and still got the segmentation fault while trying to do "contacts". Distance measurements do work however.
>
> I then took old (AMBER 8) mdcrd files generated from a small single protein and tried to get contacts. Again, got the segmentation fault. The mask .CD represented 184 atoms in 137 sets.
>
> Initially, I unpacked and first installed tooset1.4 under a user where I used gcc44, followed by installing AMBER11 using gcc44 under the same usr in the same directory. That is according to AMBER11 instructions, I had to install ToolSet1.4 first AND then AMBER11 in the same directory.
>
> However, the toolset1.4 I am now using with the new bugfixes was installed as another user in different location on computer using gcc41. I am assuming since distance measurements work that all other applications should also.
>
> ...desperately searching for a reason for the segmentation faults.
>
> Thanks, Steve
> ________________________________________
> From: Daniel Roe [daniel.r.roe.gmail.com]
> Sent: Monday, February 21, 2011 4:07 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] PTRAJ and segmentation faults
>
> 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 (gcc on Red Hat enterprise 5) and the ToolSet passed all its test. Even with the patches does ptraj have trouble with large trajectories?? I have since switched over to "netCDF" hoping this will stop the problem.
>>>
>>> Steve Seibold, Ph.D.
>>> Assistant Professor of Chemistry
>>> University of Saint Mary
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
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Received on Sun Feb 27 2011 - 12:30:04 PST
