Thank you for your respond.
I'm new in Amber. How can I solve this problem? I mean what should I do to have more residue?
>>> Carlos Simmerling <carlos.simmerling.gmail.com> 03/04/10 3:07 PM >>>
you have 1 "residue" (NRES), so cannot use more than 1 CPU.
This is the way that the parallelism in sander works.
On Thu, Mar 4, 2010 at 7:56 AM, Nkwe Monama <nmonama.csir.co.za> wrote:
> 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 - 05:30:04 PST
