AMBER Archive (2008)

Subject: Re: AMBER: Non bond list error

From: Robert Duke (
Date: Fri Oct 24 2008 - 14:04:53 CDT

Okay, WHOA. You are getting a SIGBUS error here. That is caused by either a memory addressing error or reference to an incorrectly aligned address for a datatype - depends on architecture issues for the 2nd. This indicates, most likely, an incorrectly built executable (linked to the wrong stuff perhaps), or perhaps a compiler problem (less likely). Then, looking at your new mdin, you are invoking a generalized Born implicit solvent run (igb = 1), whereas before you were attempting to use pme with explicit solvent under periodic boundary conditions. SO which did you really build - a solvated system for use with pme, or an unsolvated system for use with generalized Born? I would recommend:
1) Test sander.MPI and pmemd by running the test suites that come with amber (read the manual and README's as to how to do this stuff...)
2) Go to the and follow the tutorials link to get to some excellent tutorials written by Ross and others. Play with these for several days, and confirm that they do what they ought to be doing.
3) Then look carefully at how you built your own system and try again.
Regards - Bob Duke
(This is a resend of just my message, after the large wad of other stuff got repackaged as an attachment by symantec on my machine...)
  ----- Original Message -----
  From: neville forlemu
  Sent: Friday, October 24, 2008 2:12 PM
  Subject: Re: AMBER: Non bond list error
  I thought we had coz the executable is in one of the amber directories (/opt/brinsoft/amber8/exe/pmemd) on my machine.

  So that is what I get

  mpirun -np 4 $AMBERHOME/exe/pmemd -O -i -o minwat.out -p -c rldhn_sol.crd -r minwat.resrst -ref rldhn_sol.crd
  MPI: On host brinsvr1, Program /opt/brinsoft/amber8/exe/pmemd, Rank 0, Process 394311 received signal SIGBUS(10)

  MPI: --------stack traceback-------
  PC: 0x4045080 MPI_SGI_stacktraceback in /usr/lib32/
  PC: 0x40455a8 first_arriver_handler in /usr/lib32/
  PC: 0x4045858 slave_sig_handler in /usr/lib32/
  PC: 0xfaf064c _sigtramp in /usr/lib32/
  PC: 0x1001d6a8 in /opt/brinsoft/amber8/exe/pmemd
  PC: 0x10079530 in /opt/brinsoft/amber8/exe/pmemd
  PC: 0x10078218 in /opt/brinsoft/amber8/exe/pmemd
  PC: 0x1005a1f4 pmemd in /opt/brinsoft/amber8/exe/pmemd
  PC: 0xad69ef4 main in /usr/lib32/

  sh: dbx: not found

  MPI: -----stack traceback ends-----
  MPI: On host brinsvr1, Program /opt/brinsoft/amber8/exe/pmemd, Rank 0, Process 394311: Dumping core on signal SIGBUS(10) into directory /usr/people/forlemu/chanel/ambtrial/amb3
  MPI: Program /opt/brinsoft/amber8/exe/pmemd, Rank 2, Process 394464: Core dump on signal SIGBUS(10) suppressed.
  MPI: Program /opt/brinsoft/amber8/exe/pmemd, Rank 3, Process 394504: Core dump on signal SIGBUS(10) suppressed.
  MPI: MPI_COMM_WORLD rank 1 has terminated without calling MPI_Finalize()
  MPI: aborting job
  MPI: Received signal 9

  However I also changed my input file to this
  # test of minimization
     maxcyc=400, imin=1, cut=12.0, igb=1, ntb=0, ntpr=10,

  And used sanders again, and the minimization seems to be working ok.

  But I have to now worry about fixing some residues and letting others move, with the above input.

  I appreciate your help

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