AMBER Archive (2008)

Subject: Re: AMBER: Non bond list error

From: neville forlemu (
Date: Fri Oct 24 2008 - 14:40:08 CDT


--- On Fri, 10/24/08, Robert Duke <> wrote:
From: Robert Duke <>
Subject: Re: AMBER: Non bond list error
Date: Friday, October 24, 2008, 2:04 PM


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
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
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 -----
  neville forlemu
  Sent: Friday, October 24, 2008 2:12
  Subject: Re: AMBER: Non bond list
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
MPI: On host brinsvr1, Program
  /opt/brinsoft/amber8/exe/pmemd, Rank 0, Process 394311 received signal

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
PC: 0x1001d6a8 in
PC: 0x10079530 in
PC: 0x10078218 in
PC: 0x1005a1f4 pmemd in
PC: 0xad69ef4 main in

sh: dbx:  not found

  -----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
  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_COMM_WORLD rank 1 has terminated without calling MPI_Finalize()
  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

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