[AMBER] about error with "Must have more residues than processors!"

From: Biao Ma <jackyma1981.gmail.com>
Date: Wed, 2 Oct 2013 01:00:20 +0900

Hi, all.

I plan to run my CpHMD job on 208 processors at 26 nodes, but it's stopped
with Error "Must have more residues than processors!"
Now I redo the job on 80 processors and no problem.

Could anyone explain the reason of the error?
Weather the number of processors cannot more than the numbers of system's
residues?

A part of mdout:(I also attach the mdout and log file to make more
information)


          -------------------------------------------------------
          Amber 12 SANDER 2012
          -------------------------------------------------------

| Run on 10/02/2013 at 00:16:02
  [-O]verwriting output

File Assignments:
| MDIN: heat.mdin

| MDOUT: 1ag2.heat.mdout

|INPCRD: 1ag2.min.rst7

| PARM: 1ag2.parm7

|RESTRT: 1ag2.heat.rst7

| REFC: 1ag2.min.rst7

| MDVEL: mdvel

| MDEN: mden

| MDCRD: 1ag2.heat.mdcrd

|MDINFO: mdinfo

| MTMD: mtmd

|INPDIP: inpdip

|RSTDIP: rstdip


|INPTRA: inptraj

|

 Here is the input file:

Implicit solvent constant pH initial heating mdin

 &cntrl

    imin=0, irest=0, ntx=1,

    ntpr=500, ntwx=500, nstlim=1000000,

    dt=0.002, ntt=3, tempi=10,

    temp0=300, tautp=2.0, ig=-1,

    ntp=0, ntc=2, ntf=2, cut=30,

    ntb=0, igb=2, tol=0.000001,

    nrespa=1, saltcon=0.1, icnstph=1,

    ntcnstph=100000000,

    gamma_ln=5.0, ntwr=500, ioutfm=1,

    nmropt=1, ntr=1, restraint_wt=2.0,

    restraintmask='.CA,C,O,N',

  /

 &wt

    TYPE='TEMP0', ISTEP1=1, ISTEP2=500000,

    VALUE1=10.0, VALUE2=300.0,

  /

 &wt TYPE='END' /


--------------------------------------------------------------------------------
   1. RESOURCE USE:
--------------------------------------------------------------------------------

| Flags: MPI

| New format PARM file being parsed.
| Version = 1.000 Date = 10/01/13 Time = 16:36:54
 NATOM = 1717 NTYPES = 14 NBONH = 853 MBONA = 885
 NTHETH = 1885 MTHETA = 1197 NPHIH = 3799 MPHIA = 2875
 NHPARM = 0 NPARM = 0 NNB = 9346 NRES = 103
 NBONA = 885 NTHETA = 1197 NPHIA = 2875 NUMBND = 44
 NUMANG = 106 NPTRA = 41 NATYP = 26 NPHB = 0
 IFBOX = 0 NMXRS = 24 IFCAP = 0 NEXTRA = 0
 NCOPY = 0

 Implicit solvent radii are H(N)-modified Bondi radii (mbondi2)


| Memory Use Allocated
| Real 112087
| Hollerith 5256
| Integer 110696
| Max Pairs 1
| nblistReal 0
| nblist Int 0
| Total 1328 kbytes

| Note: 1-4 EEL scale factors are being read from the topology file.

| Note: 1-4 VDW scale factors are being read from the topology file.
| Duplicated 0 dihedrals
| Duplicated 0 dihedrals
Note: ig = -1. Setting random seed based on wallclock time in microseconds
      and disabling the synchronization of random numbers between tasks
      to improve performance.
......
......
  5. REFERENCE ATOM COORDINATES

  defa
     Mask .CA,C,O,N; matches 412 atoms

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

defa

 begin time read from input coords = 0.000 ps



           Begin reading energy term weight changes/NMR restraints
 WEIGHT CHANGES:
 TEMP0 1 500000 10.000000 300.000000 0 0

 RESTRAINTS:
                          ** No restraint defined **

                  Done reading weight changes/NMR restraints


 Number of triangulated 3-point waters found: 0
 Must have more residues than processors!


Thanks a lot!

Jacky


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Received on Tue Oct 01 2013 - 09:30:04 PDT
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