Thanks
Bob
--- On Fri, 10/24/08, Robert Duke <rduke.email.unc.edu> wrote:
From: Robert Duke <rduke.email.unc.edu>
Subject: Re: AMBER: Non bond list error
To: amber.scripps.edu
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
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 ambermd.org 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
To: amber.scripps.edu
Sent: Friday, October 24, 2008 2:12
PM
Subject: Re: AMBER: Non bond list
error
Hi
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 minwat.in -o
minwat.out -p rldhn_sol.top -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/libmpi.so
PC: 0x40455a8
first_arriver_handler in /usr/lib32/libmpi.so
PC: 0x4045858
slave_sig_handler in /usr/lib32/libmpi.so
PC: 0xfaf064c _sigtramp in
/usr/lib32/libc.so.1
PC: 0x1001d6a8
SETUP_CRD_IDX_LST_TBL.in.EW_DIRECT_CIT_MODULE in
/opt/brinsoft/amber8/exe/pmemd
PC: 0x10079530
DO_INITIAL_ATOM_DIVISION_CIT.in.ALLTASKS_SETUP_MODULE in
/opt/brinsoft/amber8/exe/pmemd
PC: 0x10078218
ALLTASKS_SETUP.in.ALLTASKS_SETUP_MODULE in
/opt/brinsoft/amber8/exe/pmemd
PC: 0x1005a1f4 pmemd in
/opt/brinsoft/amber8/exe/pmemd
PC: 0xad69ef4 main in
/usr/lib32/libftn.so
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
&cntrl
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
Neville
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Received on Sun Oct 26 2008 - 05:08:43 PDT
