Dear Carlos,
Please find below the output file of sander:
************************************************
-------------------------------------------------------
Amber 10 SANDER 2008
-------------------------------------------------------
| Run on 03/03/2010 at 16:24:02
[-O]verwriting output
File Assignments:
| MDIN: boxeq.mdin
| MDOUT: tmpmd38.mdout
|INPCRD: 1037.mrst
| PARM: 3aibx.prmtop
|RESTRT: 1038.mdrst
| REFC: refc
| MDVEL: mdvel
| MDEN: en100000to110000ps
| MDCRD: crd100000to110000ps
|MDINFO: mdinfo
|INPDIP: inpdip
|RSTDIP: rstdip
|INPTRA: inptraj
|
Here is the input file:
molecular dynamics in vacuo
&cntrl
imin = 0, irest = 1, ntx = 7, cut = 12,
igb=0, ntb=0, tempi = 0.0, temp0 = 300.0,
ntt = 3, gamma_ln = 1.0,
nstlim = 5000000, dt = 0.002,
ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500,
/
--------------------------------------------------------------------------------
1. RESOURCE USE:
--------------------------------------------------------------------------------
| Flags: MPI
| NONPERIODIC ntb=0 and igb=0: Setting up nonperiodic simulation
|Largest sphere to fit in unit cell has radius = 35.484
| New format PARM file being parsed.
| Version = 1.000 Date = 01/28/08 Time = 22:31:57
NATOM = 117 NTYPES = 6 NBONH = 62 MBONA = 59
NTHETH = 134 MTHETA = 100 NPHIH = 244 MPHIA = 143
NHPARM = 0 NPARM = 0 NNB = 689 NRES = 1
NBONA = 59 NTHETA = 100 NPHIA = 143 NUMBND = 8
NUMANG = 15 NPTRA = 6 NATYP = 7 NPHB = 0
IFBOX = 0 NMXRS = 117 IFCAP = 0 NEXTRA = 0
NCOPY = 0
| Memory Use Allocated
| Real 7381
| Hollerith 705
| Integer 30910
| Max Pairs 6786
| nblistReal 1404
| nblist Int 188266
| Total 954 kbytes
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
--------------------------------------------------------------------------------
2. CONTROL DATA FOR THE RUN
--------------------------------------------------------------------------------
ABX
General flags:
imin = 0, nmropt = 0
Nature and format of input:
ntx = 7, irest = 1, ntrx = 1
Nature and format of output:
ntxo = 1, ntpr = 500, ntrx = 1, ntwr = 500
iwrap = 0, ntwx = 500, ntwv = 0, ntwe = 500
ioutfm = 0, ntwprt = 0, idecomp = 0, rbornstat= 0
Potential function:
ntf = 1, ntb = 0, igb = 0, nsnb = 25
ipol = 0, gbsa = 0, iesp = 0
dielc = 1.00000, cut = 12.00000, intdiel = 1.00000
scnb = 2.00000, scee = 1.20000
Frozen or restrained atoms:
ibelly = 0, ntr = 0
Molecular dynamics:
nstlim = 5000000, nscm = 1000, nrespa = 1
t = 0.00000, dt = 0.00200, vlimit = 20.00000
Langevin dynamics temperature regulation:
ig = 71277
temp0 = 300.00000, tempi = 0.00000, gamma_ln= 1.00000
| MPI Timing options:
| profile_mpi = 0
| INFO: Old style inpcrd file read
--------------------------------------------------------------------------------
3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------
ABX
begin time read from input coords = 50000.000 ps
Number of triangulated 3-point waters found: 0
Must have more residues than processors!
*****************************************************************
Regards,
Nkwe
>>> Carlos Simmerling <carlos.simmerling.gmail.com> 03/04/10 2:25 PM >>>
sander gives the message that you have more processors than residues. What
does your sander output say?
It looks like you are getting more MPI threads than the # of cores you
assigned (8).
On Thu, Mar 4, 2010 at 6:05 AM, Nkwe Monama <nmonama.csir.co.za> wrote:
> Dear,
>
> I have been trying to run Amber with MOAB script and I get the following
> messages:
>
> stderr:
>
> ********************************************************************************
> MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
> with errorcode 1.
>
> NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
> You may or may not see output from other processes, depending on
> exactly when Open MPI kills them.
> --------------------------------------------------------------------------
> --------------------------------------------------------------------------
> mpirun has exited due to process rank 18 with PID 19339 on
> node cnode-1-19 exiting without calling "finalize". This may
> have caused other processes in the application to be
> terminated by signals sent by mpirun (as reported here).
> --------------------------------------------------------------------------
> [cnode-3-23:11079] 47 more processes have sent help message
> help-mpi-api.txt / mpi-abort
> [cnode-3-23:11079] Set MCA parameter "orte_base_help_aggregate" to 0 to see
> all help / error messages
>
> *********************************************************************************
>
> stdout:
>
>
> *********************************************************************************
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> Must have more residues than processors!
> ***************************************************************************
>
> The following is my MOAB script to run amber:
> ***************************************************************************
> ###These lines are for Moab
> #MSUB -l nodes=1:ppn=8
> #MSUB -l partition=ALL
> #MSUB -l walltime=2:00:00
> #MSUB -m be
> #MSUB -V
> #MSUB -o /export/home/nmonama/scratch/amber/amber.out
> #MSUB -e /export/home/nmonama/scratch/amber/amber.err
> #MSUB -d /export/home/nmonama/scratch/amber
> #MSUB -mb
> #MSUB -M nmonama.csir.co.za
>
> ##### Running commands
> cd /export/home/nmonama/scratch/amber
> mpirun -nolocal -hostfile hosts /export/home/nmonama/amber/bin/sander.MPI
> -O -i boxeq.mdin -c 1037.mrst -p 3aibx.prmtop -o tmpmd38.mdout -r 1038.mdrst
> -x crd100000to110000ps -e en100000to110000ps
>
> ****************************************************************************************
>
> Regards,
> Nkwe
>
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Received on Thu Mar 04 2010 - 05:00:03 PST
