AMBER Archive (2007)

Subject: Re: AMBER: signal SIGSEGV(11)

From: Pankaj R. Daga (pdaga_at_olemiss.edu)
Date: Tue Apr 24 2007 - 09:55:14 CDT

Hi Amber community,

I have followed suggestion given by Chris to check if there is something wrong about my protein file during minimization. But I found after 1300 cycles of minimization, the protein-ligand complex is fine and there is no problem with the structure.

Then I tried to use only steepest descent method (ntmin = 2) and found that the minimization with ntmin = 2 finishes without any error. But when I used the output file for further minimization with conjugate gradient method, I face same error once again.

************************************************

 MPI: On host redwood, Program /usr/local/appl/Amber8/exe/sander, Rank
 0, Process 17288 received signal SIGSEGV(11)
 
 MPI: --------stack traceback-------
 sh: line 1: idb: command not found

 MPI: -----stack traceback ends-----
 MPI: On host redwood, Program /usr/local/appl/Amber8/exe/sander, Rank 0, Process 17288: Dumping core on signal SIGSEGV(11) into directory /work1/r1029/HDP_APR07
 MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
 MPI: aborting job
 MPI: Received signal 11
************************************************

I am still confused, if this error is related to protein structure, related to mpi or related to sander.

I would appreciate if you could help me out.

Thanks and Regards

Pankaj

===================================================================
If your ship doesn't come in, swim out to it.......Jonathan Winters
===================================================================
Pankaj R. Daga |
Department of Medicinal Chemistry | e-mail: pdaga_at_olemiss.edu
417 Faser Hall, School of Pharmacy | fax: +1-662-915-5638
University of Mississippi | phone: +1-662-915-1853
University, MS, 38677-1848 |
===================================================================
----- Original Message -----
From: "Chris Moth" <chris.moth_at_vanderbilt.edu>
To: <amber_at_scripps.edu>
Sent: Wednesday, April 18, 2007 3:22 PM
Subject: Re: AMBER: signal SIGSEGV(11)

> There is a chance you might find it helpful to set maxcyc to 1300 so
> that you can get final output, and take a look (visualize) the
> structure. Though the energies may look reasonable, looking at the
> structure, relative to start structure, could be informative.
> Especially look around the atoms that are listed in the output file
> often. What is going on near CG atom 4880? H1 atom 6532?
>
> If you strongly suspect the minimization algorithm is essentially
> failing, then perhaps setting input for "always use steepest descent"
> (ntmin=2) would get you to an coordinate set, from which conjugate
> gradient performs better.
>
> I'm not predicting either of the above will be successful :) - but they
> are quick things I might "try" to move ahead if I were stuck.
>
> C
>
> Pankaj R. Daga wrote:
>> Hi Dr. Case and Dr. Ross,
>>
>> Thank you very much for your inputs. I have tried to run same job with
>> single processor. But I am still facing the same error.
>>
>> The protein I am dealing with is a homology model of enzyme and it is
>> a ternary complex of enzyme-DNA-ligand. The ternary system is solvated
>> in TIP3PBOX. My aim is to run MD simulation on optimized system.
>> Hence, I started with stepwise minimization.
>>
>> First step minimization went well but when I submitted the output file
>> from first step minimization for the next step, sander minimizes the
>> molecule for few steps (1300 out of 5000). Then I face this error.
>> This error is reprodicible. I am attaching the input file and output
>> file here.
>>
>>
>> ************************************************
>>
>> MPI: On host redwood, Program /usr/local/appl/Amber8/exe/sander, Rank
>> 0, Process 17288 received signal SIGSEGV(11)
>>
>>
>> MPI: --------stack traceback-------
>> sh: line 1: idb: command not found
>>
>> MPI: -----stack traceback ends-----
>> MPI: On host redwood, Program /usr/local/appl/Amber8/exe/sander, Rank
>> 0, Process 17288: Dumping core on signal SIGSEGV(11) into directory
>> /work1/r1029/HDP_APR07
>> MPI: MPI_COMM_WORLD rank 0 has terminated without calling MPI_Finalize()
>> MPI: aborting job
>> MPI: Received signal 11
>
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