Do you have just 1 residue in your system? If so then the error message is
correct, there must be more residues than processors and you have 1
processor and 1 residue. Using the serial code will avoid this issue.
If you have more than this then we would need to see your various input
files to be able to debug any further.
All the best
Ross
> -----Original Message-----
> From: amber-bounces.ambermd.org [mailto:amber-bounces.ambermd.org] On
> Behalf Of Nkwe Monama
> Sent: Friday, March 05, 2010 6:47 AM
> To: amber.ambermd.org
> Subject: Re: [AMBER] Errors while running Amber
>
> Dear Robert,
>
> I used sander.MPI
>
> Regards,
> Nkwe
>
> >>> "Robert Duke" <rduke.email.unc.edu> 03/05/10 3:57 PM >>>
> It looks to me like you are attempting a pme simulation on a single
> residue
> without any solvent present. Due to workload division issues in
> parallel
> runs, especially for sander, you need at least 1 residue in your system
> per
> processor in use (may actually be more; I don't remember the exact
> code).
> So it makes sense to run implicit solvent methods like generalized Born
> without solvent, but this is generally not true for explicit solvent
> methods
> like pme, and that leads me to believe you need to go to the amber
> website,
> ambermd.org, and spend some time running the tutorials there as well as
> reading the amber manual. But my point about explicit solvent - if you
> had
> solvated the system, then you would have a LOT of "residues" (actually
> molecules) in the solvent, and that is when it becomes profitable to
> run on
> lots of processors. Incidentally, it looks to me in the output below
> like
> you actually attempted the run on 48 processors. Did you use sander,
> not
> sander.MPI?
> Regards - Bob Duke
> ----- Original Message -----
> From: "Nkwe Monama" <nmonama.csir.co.za>
> To: <amber.ambermd.org>; <carlos.simmerling.gmail.com>
> Sent: Friday, March 05, 2010 4:17 AM
> Subject: Re: [AMBER] Errors while running Amber
>
>
> 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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