I have used 1 processor and I'm still getting the "Must have more residues than processors!" errror message. My stderr is as follows:
********************************************************
MPI_ABORT was invoked on rank 1 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 1 with PID 896 on
node cnode-1-2 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-3-32:09019] 47 more processes have sent help message help-mpi-api.txt / mpi-abort
[cnode-3-32:09019] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
*******************************************************************
and the output for sander is:
**************************************************
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 3:27 PM >>>
the system you simulate should be determined by what you want to learn. I
would not change it just to use more processors.
to sove it, just use 1 processor. you could add more residues but I'm not
sure why using more processors should make you want to change your system.
On Thu, Mar 4, 2010 at 8:17 AM, Nkwe Monama <nmonama.csir.co.za> wrote:
> 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 Fri Mar 05 2010 - 01:30:03 PST
