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
>>
>> _______________________________________________
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>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
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Received on Sun Feb 27 2011 - 11:00:05 PST
