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PostPosted: Wed Oct 11, 2017 6:28 pm 
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Joined: Fri Jan 20, 2017 5:29 pm
Posts: 38
Location: Graduate School of Oceanography,URI
Hi all
I am testing an idealized grid by uncoupled COAWST (only roms), But I got an error which related to "out of bound", I don't know how to solve this problem, Can anyone help me? The log file is :
Code:
/home/zhou/COAWST/Projects/Idealized_Mount_Hope/DeBug/uncoupled

 Model Input Parameters:  ROMS/TOMS version 3.7 
                          Wednesday - October 11, 2017 -  2:16:20 PM
 -----------------------------------------------------------------------------

 Inelt Test Debug Case

 Operating system : Linux
 CPU/hardware     : x86_64
 Compiler system  : gfortran
 Compiler command : /opt/mpich2/bin/mpif90
 Compiler flags   : -frepack-arrays -g -fbounds-check -I/usr/include -ffree-form -ffree-line-length-none

 Input Script  :

 SVN Root URL  : https:://myroms.org/svn/src
 SVN Revision  : 1185M

 Local Root    : /home/zhou/COAWST
 Header Dir    : /home/zhou/COAWST/Projects/Idealized_Mount_Hope/DeBug/uncoupled
 Header file   : inlet_test.h
 Analytical Dir: /home/zhou/COAWST/Projects/Idealized_Mount_Hope/DeBug/uncoupled

 Resolution, Grid 01: 0098x0398x008,  Parallel Nodes:  16,  Tiling: 004x004


 Physical Parameters, Grid: 01
 =============================

        720  ntimes            Number of timesteps for 3-D equations.
     60.000  dt                Timestep size (s) for 3-D equations.
         20  ndtfast           Number of timesteps for 2-D equations between
                                 each 3D timestep.
          1  ERstr             Starting ensemble/perturbation run number.
          1  ERend             Ending ensemble/perturbation run number.
          0  nrrec             Number of restart records to read from disk.
          T  LcycleRST         Switch to recycle time-records in restart file.
        720  nRST              Number of timesteps between the writing of data
                                 into restart fields.
          1  ninfo             Number of timesteps between print of information
                                 to standard output.
          1  nSTA              Number of timesteps between the writing of data
                                 the stations file.
          T  ldefout           Switch to create a new output NetCDF file(s).
         60  nHIS              Number of timesteps between the writing fields
                                 into history file.
          0  nQCK              Number of timesteps between the writing fields
                                 into quicksave file.
          1  ntsAVG            Starting timestep for the accumulation of output
                                 time-averaged data.
         60  nAVG              Number of timesteps between the writing of
                                 time-averaged data into averages file.
          1  ntsDIA            Starting timestep for the accumulation of output
                                 time-averaged diagnostics data.
         60  nDIA              Number of timesteps between the writing of
                                 time-averaged data into diagnostics file.
 1.0000E-03  nl_visc2          NLM Horizontal, harmonic mixing coefficient
                                 (m2/s) for momentum.
          F  LuvSponge         Turning OFF sponge on horizontal momentum.
          F  LtracerSponge(01) Turning OFF sponge on tracer 01: temp
          F  LtracerSponge(02) Turning OFF sponge on tracer 02: salt
 5.0000E-06  Akt_bak(01)       Background vertical mixing coefficient (m2/s)
                                 for tracer 01: temp
 5.0000E-06  Akt_bak(02)       Background vertical mixing coefficient (m2/s)
                                 for tracer 02: salt
 5.0000E-05  Akv_bak           Background vertical mixing coefficient (m2/s)
                                 for momentum.
 5.0000E-06  Akk_bak           Background vertical mixing coefficient (m2/s)
                                 for turbulent energy.
 5.0000E-06  Akp_bak           Background vertical mixing coefficient (m2/s)
                                 for turbulent generic statistical field.
      3.000  gls_p             GLS stability exponent.
      1.500  gls_m             GLS turbulent kinetic energy exponent.
     -1.000  gls_n             GLS turbulent length scale exponent.
 7.6000E-06  gls_Kmin          GLS minimum value of turbulent kinetic energy.
 1.0000E-12  gls_Pmin          GLS minimum value of dissipation.
 5.4770E-01  gls_cmu0          GLS stability coefficient.
 1.4400E+00  gls_c1            GLS shear production coefficient.
 1.9200E+00  gls_c2            GLS dissipation coefficient.
-4.0000E-01  gls_c3m           GLS stable buoyancy production coefficient.
 1.0000E+00  gls_c3p           GLS unstable buoyancy production coefficient.
 1.0000E+00  gls_sigk          GLS constant Schmidt number for TKE.
 1.3000E+00  gls_sigp          GLS constant Schmidt number for PSI.
   1400.000  charnok_alpha     Charnok factor for Zos calculation.
      0.500  zos_hsig_alpha    Factor for Zos calculation using Hsig(Awave).
      0.250  sz_alpha          Factor for Wave dissipation surface tke flux .
    100.000  crgban_cw         Factor for Craig/Banner surface tke flux.
      0.000  wec_alpha         WEC factor for roller/breaking energy distribution.
 3.0000E-04  rdrg              Linear bottom drag coefficient (m/s).
 2.5000E-02  rdrg2             Quadratic bottom drag coefficient.
 1.5000E-02  Zob               Bottom roughness (m).
 5.0000E-01  Zos               Surface roughness (m).
          1  Vtransform        S-coordinate transformation equation.
          1  Vstretching       S-coordinate stretching function.
 1.0000E+00  theta_s           S-coordinate surface control parameter.
 1.0000E+00  theta_b           S-coordinate bottom  control parameter.
      0.000  Tcline            S-coordinate surface/bottom layer width (m) used
                                 in vertical coordinate stretching.
   1025.000  rho0              Mean density (kg/m3) for Boussinesq approximation.
      0.000  dstart            Time-stamp assigned to model initialization (days).
       0.00  time_ref          Reference time for units attribute (yyyymmdd.dd)
 0.0000E+00  Tnudg(01)         Nudging/relaxation time scale (days)
                                 for tracer 01: temp
 0.0000E+00  Tnudg(02)         Nudging/relaxation time scale (days)
                                 for tracer 02: salt
 9.0000E+01  Tnudg_SSS         Nudging/relaxation time scale (days)
                                 for sea surface salinity.
 0.0000E+00  Znudg             Nudging/relaxation time scale (days)
                                 for free-surface.
 0.0000E+00  M2nudg            Nudging/relaxation time scale (days)
                                 for 2D momentum.
 0.0000E+00  M3nudg            Nudging/relaxation time scale (days)
                                 for 3D momentum.
 0.0000E+00  obcfac            Factor between passive and active
                                 open boundary conditions.
          F  VolCons(1)        NLM western  edge boundary volume conservation.
          F  VolCons(2)        NLM southern edge boundary volume conservation.
          F  VolCons(3)        NLM eastern  edge boundary volume conservation.
          F  VolCons(4)        NLM northern edge boundary volume conservation.
     10.000  T0                Background potential temperature (C) constant.
     30.000  S0                Background salinity (PSU) constant.
   1027.000  R0                Background density (kg/m3) used in linear Equation
                                 of State.
 1.7000E-04  Tcoef             Thermal expansion coefficient (1/Celsius).
 7.6000E-04  Scoef             Saline contraction coefficient (1/PSU).
      1.000  gamma2            Slipperiness variable: free-slip (1.0) or
                                                      no-slip (-1.0).
          F  LuvSrc            Turning OFF momentum point Sources/Sinks.
          F  LwSrc             Turning OFF volume influx point Sources/Sinks.
          F  LtracerSrc(01)    Turning OFF point Sources/Sinks on tracer 01: temp
          F  LtracerSrc(02)    Turning OFF point Sources/Sinks on tracer 02: salt
          F  LsshCLM           Turning OFF processing of SSH climatology.
          F  Lm2CLM            Turning OFF processing of 2D momentum climatology.
          F  Lm3CLM            Turning OFF processing of 3D momentum climatology.
          F  LtracerCLM(01)    Turning OFF processing of climatology tracer 01: temp
          F  LtracerCLM(02)    Turning OFF processing of climatology tracer 02: salt
          F  LnudgeM2CLM       Turning OFF nudging of 2D momentum climatology.
          F  LnudgeM3CLM       Turning OFF nudging of 3D momentum climatology.
          F  LnudgeTCLM(01)    Turning OFF nudging of climatology tracer 01: temp
          F  LnudgeTCLM(02)    Turning OFF nudging of climatology tracer 02: salt

          T  Hout(idBath)      Write out time-dependent bathymetry.
          T  Hout(idFsur)      Write out free-surface.
          T  Hout(idUbar)      Write out 2D U-momentum component.
          T  Hout(idVbar)      Write out 2D V-momentum component.
          T  Hout(idUvel)      Write out 3D U-momentum component.
          T  Hout(idVvel)      Write out 3D V-momentum component.
          T  Hout(idWvel)      Write out W-momentum component.
          T  Hout(idOvel)      Write out omega vertical velocity.
          T  Hout(idTvar)      Write out tracer 01: temp
          T  Hout(idTvar)      Write out tracer 02: salt
          T  Hout(idpthR)      Write out time-varying dephts of RHO-points.
          T  Hout(idpthU)      Write out time-varying dephts of U-points.
          T  Hout(idpthV)      Write out time-varying dephts of V-points.
          T  Hout(idpthW)      Write out time-varying dephts of W-points.
          T  Hout(idVvis)      Write out vertical viscosity: AKv.

          T  Dout(M2sstr)      Write out 2D momentum surface stress.
          T  Dout(M2bstr)      Write out 2D momentum bottom stress.


 Output/Input Files:

             Output Restart File:  ocean_rst.nc
             Output History File:  ocean_his_coupled.nc
            Output Averages File:  ocean_avg_coupled.nc
         Output Diagnostics File:  ocean_dia.nc
            Output Stations File:  ocean_sta.nc
                 Input Grid File:  /home/zhou/COAWST/Projects/Idealized_Mount_Hope/Grid/idealized_mount_hope_grid_50m.nc
At line 2929 of file read_phypar.f90
Fortran runtime error: Array reference out of bounds for array 'frc', upper bound of dimension 1 exceeded (1 > 0)
aborting job:
Fatal error in MPI_Bcast: Other MPI error, error stack:
MPI_Bcast(821): MPI_Bcast(buf=0x1623330, count=1, MPI_INTEGER, root=0, MPI_COMM_WORLD) failed
MPIR_Bcast(197):
MPIC_Recv(98):
MPIC_Wait(308):
MPIDI_CH3_Progress_wait(207): an error occurred while handling an event returned by MPIDU_Sock_Wait()
MPIDI_CH3I_Progress_handle_sock_event(492):
connection_recv_fail(1728):
MPIDU_Socki_handle_read(590): connection closed by peer (set=0,sock=1)
[mpiexec@n008.cluster.com] HYDT_bscd_pbs_wait_for_completion (tools/bootstrap/external/pbs_wait.c:67): tm_poll(obit_event) failed with TM error 17002
[mpiexec@n008.cluster.com] HYDT_bsci_wait_for_completion (tools/bootstrap/src/bsci_wait.c:23): launcher returned error waiting for completion
[mpiexec@n008.cluster.com] HYD_pmci_wait_for_completion (pm/pmiserv/pmiserv_pmci.c:218): launcher returned error waiting for completion
[mpiexec@n008.cluster.com] main (ui/mpich/mpiexec.c:344): process manager error waiting for completion

The line 2929 of file read_phypar.f90 is :
Code:
          DO i=1,nFfiles(ng)
            DO ifile=1,FRC(i,ng)%Nfiles
              fname=FRC(i,ng)%files(ifile)
              IF (.not.find_file(ng, fname, 'FRCNAME')) GO TO 30
              IF (ifile.eq.1) THEN
                WRITE (out,310) '         Input Forcing File ', i,      &
     &                          ':  ', TRIM(fname)
              ELSE
                WRITE (out,'(35x,a)') TRIM(fname)
              END IF
            END DO
          END DO


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PostPosted: Wed Oct 11, 2017 6:41 pm 
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Joined: Wed Jul 02, 2003 5:29 pm
Posts: 3264
Location: IMS/UAF, USA
Quote:
FRC(i,ng)
This array gets allocated when the model reads the first of these lines:
Code:
    NFFILES == 13                          ! number of forcing files

    FRCNAME == /center/d/kate/MERRA_drowned/drowned_MERRA_Pair_3hours_2004.nc   |
               /center/d/kate/MERRA_drowned/drowned_MERRA_Pair_3hours_2005.nc \
               /center/d/kate/MERRA_drowned/drowned_MERRA_Qair_3hours_2004.nc |
               /center/d/kate/MERRA_drowned/drowned_MERRA_Qair_3hours_2005.nc \
               /center/d/kate/MERRA_drowned/drowned_MERRA_Tair_3hours_2004.nc |
                 :
It has to be allocated before you get to the rest of these lines, which use the array.


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